These are my rankings of Doctor Who stories from the First Doctor period. I have categorized them into five categories, rather than finding a linear ranking order for each story. For links to the entire series, see here.
Cream of the Crop
10. The Dalek Invasion of Earth: One of the best First Doctor stories. It's the second appearance of the Daleks, and given the original naming conventions (where individual episodes were named, not overall serials, as became standard practice later in the show) you wouldn't have gotten the presence of the Daleks spoiled by the title until the end of the first episode. The TARDIS crew ends up in 22nd Century London, where the city has been devastated, with very few people in sight, all of them acting in a robotic manner. When they discover the first Dalek they come across, it's a bit of a shock, because they'd only met the Daleks on their home planet in their first appearance. Despite a ridiculous sci-fi premise for why the Daleks have invaded Earth, this story works incredibly well, which certainly isn't true of all the Terry Nation Dalek stories in this period. I don't think it's his best. That honor goes to The Daleks' Master Plan. But this is among the truly classic stories of the First Doctor period.
21. The Daleks' Master Plan: This is by far my favorite First Doctor story. A full dozen episodes (a baker's dozen, if you count the prologue episode Mission to the Unknown, which came two stories before but was really part of this story). Unfortunately, only three episodes survive, so you either have to listen to the soundtracks for the rest or watch the fan-created reconstructions based on the large number of set photos that exist and the existing soundtracks. But it's worth it. The stakes are higher than any previous Dalek story, and it has better good science fiction concepts than many of the other non-historical earlier episodes. We get to see a future Earth empire with a military that knows all about the Daleks and is trained to fight them, including two noteworthy characters, a brother and sister played by Nicholas Courtney, who later went on to play Brigadier Lethbridge-Stewart, and Jean Marsh as Sara Kingdom, one of my favorite companions over the entire run of the origianl series. Marsh also had earlier played Princess Joanna in The Crusade and much later returned to play Morgana in the Seventh Doctor story Battlefield, which was also the final appearance of Brigadier Lethbridge-Stewart in the Doctor Who show. This was the only story featuring Sara Kingdom, unfortunately, but she's present for something like eight or nine episodes of it. Terry Nation wrote episodes 1-5 and 7. Unfortunately, the seventh was a Christmas episode that has nothing to do with the rest of the story, which is its only real low point. By that point in the story, we're reliving The Chase, where the Doctor, The Meddling Monk (from The Time Meddler), and the Daleks are running around through time, and it slows down a bit, but those parts are a little better than the middle episodes of The Chase in my view. But the first half of this story and the last two or three episodes are as enjoyable as the First Doctor gets, even with reconstructions of the episodes.
23. The Ark: This is one of the better "future of humans" stories of the First Doctor. The TARDIS appears on a human ship in the future, and there's another intelligent species serving humans as slaves, in effect, although from all appearances it's consensual, and the humans are unaware of the full intelligence of these beings. Halfway through, the TARDIS crew has resolved their original problem keeping them there, and they reappear in the same spot but much further in the future. Since this is a time when the Doctor had no control at all over where the TARDIS ends up, that seems remarkably odd. Then they discover that a revolution has occurred, and the other species has turned the tables on their human masters. Instead of being victims that we feel sorry for, they are now the villains. This was a nice nod to the common phenomenon in human history of the victims gaining control and becoming just as bad oppressors as those who had oppressed them. We also get to see an invisible (i.e. money-saving) but very powerful alien race that reminded me much of the sort of thing you might see on the original series of Star Trek, which was being made around the same time period as this episode. This episode didn't win me over to new companion Dodo. But it has some funny moments between her and the Doctor, where her slang expressions (that are entirely commonplace now, to a point where it shocked me that anyone wouldn't be used to it) give us a glimpse of the First Doctor's cantankerous nature in his complaints that she's not speaking English (which I should note is her first language and not his). And this is one of the few First Doctor stories that I'd gladly show to someone who wanted to see a good example of what the best of his period was like.
Very Enjoyable Stories
2. The Daleks (AKA The Mutants, not to be confused with a later Third Doctor story): This is the serial that gave the show its initial success. It drags a bit about 3/4 of the way through, but overall this is a great introduction to the Daleks. As with most of Terry Nation's Doctor Who stories, there are deeper themes to the story than just an action/adventure romp. In contrast to some of the emphasis of later Doctor Who stories (including some of Nation's own), here we see the Doctor encouraging pacifists to take up arms to destroy a menace that would otherwise end up destroying them. This is one of the best First Doctor stories.
17. The Time Meddler: In this story we get the introduction of our first Time Lord character (not that we have that name yet) besides the Doctor and Susan, and we even get to see his TARDIS, both inside and out. His chameleon circuit works, so we see a TARDIS properly disguised. The Meddling Monk returns as well in the Daleks' Master Plan, so he's also a recurring villain. A renegade Time Lord seeking to change history for some unclear profit motive (or perhaps for some higher good, but in any case the Doctor disapproves), the Meddling Monk has set himself up at a monastery, where he's pretending a whole group of monks are present by using future technology (including a phonograph with recordings of medieval-style chant) to give the appearance of a larger population of monks (as well as to make his stay more comfortable with appliances such as a toaster). The Doctor and his companions eventually figure out what's going on, and the Doctor manages to show some know-how when it comes to how a TARDIS works by sabotaging the Monk's TARDIS (which unfortunately never manages to help him get his TARDIS working properly again so he can actually control where it goes, not until the Time Lords help him later on during the Third Doctor period). This is the first time we see a historical setting with something non-historical worked in, a formula that the show eventually uses almost exclusively for stories taking place in the Earth's past, but we still have another season or so of purely historical episodes to go before that becomes standard. It's the first time also for the new lineup of the Doctor, Vicki, and Steven. It has some moments of lagging, as historical episodes tend to do, and it's the first historical episode with discussion of the real possibility of history-changing (see The Space Museum for the first instance of this, however, although this doesn't have the complete incoherence of that story). That is a disappointment from the perspective of metaphysics, but the unique elements of this story more than make up for it.
27. The War Machines: This is one of my favorite. If it weren't for the musical companions, it would be in the top category. The adventure starts with the Doctor and Dodo arriving in Dodo's own time period (roughly the time the episode aired). She's in the first episode and maybe part of the second. She never even appears to say goodbye to the Doctor. It introduced Ben and Polly, but Polly is brainwashed for most of the episode, so we don't get to see her in her right mind very much. And much of the episode Ben hasn't really connected with the Doctor. So it's not really the usual Doctor and his companion (or companions) sort of piece. That being said, this was a great introduction to what became a much more standard format for the Second Doctor period, where the Doctor (and in the other cases his companions) is in the time period when the show was being made, the mid-late 1960s, fighting off some menace threatening the time period of the viewers of the show. In this case, it's an artificial intelligence that, in a rare case, seems to have nothing to do with aliens, but you do get some rather rudimentary-looking robot threats (in keeping with the era they couldn't have them be too sci-fi looking). The Doctor uses logical paradoxes to undo the machine, as he does in several other stories (The Green Death, Death to the Daleks, and Shada come to mind). I do tend to like Ben and Polly, but we don't see a lot of Polly in this one. There's a nice scene at the end where the Doctor thinks he's all alone for the first time since the show began, but he ends up getting surprised with some unintended stowaways at the end, leading into the next season (and his final two stories).
29. The Tenth Planet: This is the introduction of the Cybermen and the last story for the First Doctor, so there's particular significance to it, but it doesn't work as well as I'd like. The Second Doctor Cybermen stories are much better. They look like they're wearing cloth outfits instead of metal. It's hard to hear what they're saying sometimes. The Doctor is showing his age, and several of his scenes had to be given to Ben or Polly. (Both Hartnell and the character are dying of old age at this point.) At the end, after defeating the Cybermen, he just collapses and dies, only to be regenerated into the Second Doctor. They don't explain the regenaration all that well, and the final episode is missing (although there are copies of the regeneration scene that have been released on DVD and online). Fortunately, this is one of the missing episodes that have now been animated. Still, this is a decent base-under-siege story, a template that becomes much more common with the Second Doctor, and as the introduction to the Cybermen and the final First Doctor story, it's certainly one to see.
Stories With a Lot Going For Them
4. Marco Polo: Unfortunately, none of this story survives, but the reconstruction was an enjoyable watch. Too many First Doctor serials were time travel stories to Earth's past without any other science fiction elements. Most of them were relatively boring, and some of them were even not very historically accurate, which sort of defeats the original educational purpose of the show (alternately dealing with history and science with the historical and science fiction stories). But this one is perhaps the best of the bunch. It was a relatively enjoyable story, and it didn't feel to me as if it was beginning to drag even well into it, despite the fact that it was a full seven episodes long, without any live action to it (just extensive still photos from the set and the sound from the original recording). They put a lot of effort into the beautiful sets, costumes, and props. It's a shame all we have now are the still photos.
5. The Keys of Marinus: Here is Terry Nation's second Doctor Who story and his first of only two that didn't involve the Daleks. It's sort of a hodge-podge, with each episode serving as a different adventure in a different part of the same planet, contributing toward an overall quest. The first episode was especially interesting and seemed very much in the domain of good science fiction. The second involved a nice virtual reality premise, with typical Terry Nation intelligent reflection. The third attempted that with some kind of intelligent plants attacking the characters, but it seemed less interesting to me, and the fourth seemed even less so with just some kind of arctic adventure leading into caves (a device he used to make it feel adventurey in the Daleks serial in the more boring parts of the Daleks serial as well). When they got back to civilization for the final two parts, there was a nice criminal trial that eventually tied back in to the overall story in a way that didn't feel contrived. It started well and ended well, but like the Daleks it did feel stretched out, in this case probably to provide variety, but I'm not sure it worked as well in this case.
6. The Aztecs: One of the better historical stories, in my view not as good as Marco Polo, but this one entirely survives. It's slightly ambiguous between the impossibility of changing the past and the Doctor's just having a moral imperative never to do so in any way, probably just because the writing never attempted to make that distinction. The story feels less plausible to me than Marco Polo. But it held my interest more than some of the historical episodes.
8. The Reign of Terror: This is the final story of the first season, although it hadn't originally been intended that way. It's one of the better historicals, and the two missing episodes have been animated alongside the original audio for those episodes, so you no longer have to watch reconstructions to get the whole story. More care was put into making it one of the more historically reliable stories from Earth's past, and even other stories by the same author were less so (especially The Romans).
9. Planet of Giants: This one is certainly different. I believe it's the first Doctor Who story (beyond the first episode, anyway) that takes place during the time period when it was produced. And the deep irony is that two of the characters are desperately trying to get back to that time period, and the Doctor has no control over the TARDIS, which just is not bringing them back there. But in this story, they turn out to be shrunk to a fraction of their size. It's "Doctor, I Shrunk the Kids". The TARDIS crew not only has to deal with things that aren't usually threats simply because of their tiny size, but they also have to help foil a criminal plot that they at no point in the story really understand to be going on right around them. This was a four-parter whose final two episodes were edited into one, leaving out a bit of story that might have made a little more sense of things, but the producers thought it was moving too slowly as it went on. I enjoyed the novelty of the episode, but I'm glad this didn't set a precedent.
10. The Rescue: It's rare that I like a two-parter on this show, but I thought this was one of the better ones. If it had lasted any longer, I'm not sure it would have worked as well without a good deal more creativity. David Whitaker becomes one of the more important writers on the show, but his first few stories are much less memorable, and that's true of this one but perhaps a little less so than some of the others. This is the first introduction of a new companion since the first episode, and a bit of time is spent introducing Vicki, since she'll be staying with them a lot longer than you're initially supposed to expect. A nice twist on what's really going on with the monster they're experiencing, along with another twist at the end with what's going on additionally on the planet in question.
13. The Web Planet: The quality for this one makes it difficult to watch. It was filmed in the dark during a time when that never led to good results, and I wonder if the masters have degraded some as well. I do like much of the story, but it's a little hard to follow. This is the second alien world story of the second season (a full five stories in), and the first was the two-part The Rescue, so this does fill a void in the season up to this point. Some creative thought went into the aliens and the story, but the execution leaves a lot to be desired.
18. Galaxy 4: This was a largely failed attempt to have something else like the Daleks that would capture the imaginations and interests of fans. The Chumblies just don't do that. But the story isn't bad. There's a nice twist in terms of who you're supposed to expect to be the good guys and who turns out to be. A couple years ago, they found an episode. The other three are all still missing.
19. Mission to the Unknown (AKA Dalek Cutaway): In a sense, this is really the first episode of serial #20, The Daleks' Master Plan, which is my favorite story of the First Doctor. They needed a story without the main cast, I believe for scheduling reasons, and they wanted to whet people's appetites for the coming 12-part serial that brought a return to the fan favorite monsters. As a standalone story, this isn't that great, and the lack of any regular cast members really detracts from its interest. Furthermore, it sets you up for what promise to be a great story about the Daleks trying to take over the galaxy in the far future, with the Earth astronauts who stumble on the planet where their plans are being hatched all meeting an unfortunate fate but managing to get off a help message at the last minute. But then when we return to the TARDIS crew in the next episode, where they land in ancient Troy for one of the least interesting stories of the First Doctor period, and it takes four more episodes before we get back to this story. It does set up a truly great story, and watching it without that interlude is, I'm sure, much better. The CD release of the soundtrack combines these two stories without the intervening one. This episode, is, alas, lost, as is much of the 12-part story that it sets up. Three episodes exist out of the total of thirteen. This episode has, however, been animated along with the original soundtrack, and although the BBC has not allowed it to be officially released there are copies floating around the internet, along with the fan-made reconstruction based on set photos and the original audio.
26. The Savages: This is one of the more underrated First Doctor stories. Unfortunately, none of the episodes exist, but I enjoyed watching the reconstructions very much. It's a much stronger morality play than most Doctor Who at the time, and it gets into the meme of the future utopia that's not really a utopia once you dig deeper that has now become cliche, but as morality plays in science fiction in the mid-60s go, this is pretty good. There is some hokey sci-fi stuff about sucking out life essences to give everyone else happiness. That's probably what mainly keeps me from putting it up in the next category. It also has a hackneyed departure for one of my favorite First Doctor companions Steven, which is a bit of a disappointment at the end. It also gives Dodo something more to do than she usually got, and she was able to show some intelligence. Usually she just had things happen to her. But as her last full storyh, it was too little too late for her to be redeemed. On to new companions in the next story.
7. The Sensorites: I've half a mind to put all the sci-fi stories above all the historicals, but I can't do that. The Sensorites really does have its moments. There's a nice twist where the aliens that seem to be evil turn out to be completely misunderstood. We also get to see the Doctor using his scientific knowledge at length to help people, which hadn't up to this point done too much of. But the story itself didn't grab me, even if the rarer treat of having actual aliens at this point in the series was refreshing. It's not one of the more memorable of the First Doctor's alien planet stories.
12. The Romans: There's a certain brand of humor here that I'm sure older generations would appreciate more than I do. Dennis Spooner for some reason decided to do this one more as a farce, without any concern for historical accuracy, after having produced a much better historical with exactly that concern in his earlier story The Reign of Terror. One nice element of this story is seeing the TARDIS crew hanging out and relaxing for a while at the beginning, with a clear indication that they've been there for weeks, perhaps months, hanging out at the house of some wealthy Roman family who is out of town while recovering from their harrowing adventures up to this point. They end up becoming separated and get into a bunch of misadventures, which intertwine in ways that the characters never realize. It relies on legendary elements of Nero's reign and becomes a comedy of errors, despite a quite serious Roman slavery side plot. I had a hard time getting into much of it, though.
16. The Chase: After the first two excellent Dalek stories, this is a bit of a disappointment, but it does have its fun moments, and not all of it is bad. The first episode reveals that the Daleks have time travel, have discovered where the Doctor and his companions are, and are headed right there to eliminate them. A chase through space and time ensues, with some quick visits to important landmarks (the Empire State Building, the Mary Celeste), only to have to depart nearly instantly once the Daleks materialize right after them. They end up spending one episode running around chased by Daleks in a haunted house of robots, although the TARDIS crew never figures out that the monsters are robots. We see that it's a haunted house only after the TARDIS dematerializes at the end of the episode. They end up on a planet where Steven Taylor, the one lone human survivor remains from a human settlement crew, remains, after the rest of his crew has been eliminated by new robot enemies the Mechanoids, who turn out to be worthy opponents of the Daleks once the Daleks arrive. Steven acquits himself well and unfortunately appears to die at the end in a moment of heroic sacrifice, and then original companions Ian and Barbara get to use the Dalek time machine to go back to their own time at long last. It isn't until the next episode that we discover Steven has survived and stowed away on the TARDIS, and he turns out to be one of the longer-lasting First Doctor companions, as well as one of my favorites, since his knowledge of future technology and astronaut training will several times come in handy. I liked the last episode especially, but the meanderings that came before it begin to wear, even with the novelty of seeing the Daleks once again. This is my least favorite Dalek story of this period.
21. The Massacre (aka The Massacre of St Bartholemew's Eve): This is a nice instance of a historical episodes about events that I didn't know a lot about, so I actually learned a bit while watching it. It also has William Hartnell playing another character who happens to look like the Doctor (the first of, I believe, four times that the original series did this with either the Doctor or a companion: it was also done with the Second Doctor in The Enemy of the World, Romana in The Androids of Tara, and Nyssa in Black Orchid). There's also a noteworthy moment at the end of the final episode, where the Doctor and Steven land in contemporary England (i.e. the mid-60s) and accidentally picked up a new companion, Dodo, something that usually happens only at the end of an episode where the character has played a large role. This is a rare instance in the original show of a character coming in at the very end of an episode, for us to get to know in the next story. But the overall story for this one didn't do much for me.
25. The Gunfighters: This was just odd. British actors with badly-faked Texas accents doing a classic-style Western, complete with saloon songs (even one sung by companion Dodo). We get the OK corral duel with the Doctor, who hates guns, having to show up for a gunfight as a participant. I didn't think it was all that great, but it was certainly different, and all the episodes exist, which does make it more enjoyable than watching a reconstruction, other things being equal. Not one I'll place any value on rewatching, but I don't see it as among the worst of the bunch.
1. 100,000 BC (AKA "The Unearthly Child"): This is the very first Doctor Who story, and it's frankly not very good. It's interesting to see the Doctor first coming into contact with human companions, when he'd just been traveling with his granddaughter. The first episode held my interest just because it introduced all the original characters. Once they got stuck in 100,000 BC, however, it was a pretty boring adventure in cavemen times for episodes 2-4. It showed none of the promise of what a time-travel show could do, never mind the heights of science fiction excellence that later years would bring. I'm not sure the show would have gone very far if it had continued in this vein, but it took the popular success of the Daleks in the next story to secure the show's future.
3. Inside the Spaceship (AKA The Edge of Destruction): A bubble story on the TARDIS exploring the uncomfortable lack of trust between these characters who were just getting to know each other. The sci-fi premise that gets the ship intro trouble is completely ludicrous, and the characters are not all that enjoyable. This is one of the first stories I watched from the First Doctor, and I had a hard time getting through it the second time when I decided to watch them all in order. There's some character development here, though, so it is important for continuity.
14. The Crusade: One of my least favorite historical episodes, though not yet my least favorite. Nothing much happens in this story. There is a capture and release and another capture by the other side, but none of it feels very significant, and you don't get to see the Doctor and his companions contributing to events in any way. You get to see important historical characters of the time, including Richard the Lion-Hearted (played by a young Grand Maester Pycelle from Game of Thrones) and Saladin (played, unfortunately, but an English actor in Arab-face). We also get to see Jean Marsh for the first time here. She later goes on to play one of my favorite First Doctor companions, the short-lived Sarah Kingdom. You also have a very strange side-plot with Vicki being passed off as a boy because she had happened to have pants on. Perhaps these episodes would have been better if I'd seen the actual episodes of all four episodes, rather than just the two surviving episodes and reconstructions for the other two. They are planning on animated those two episodes relatively soon, last I'd heard.
15. The Space Museum: This is the first attempt in Doctor Who to do something interesting with time travel, i.e. what the later series calls timey-wimey. Unfortunately, it's a complete failure. The TARDIS crew finds themselves in a space museum, quite literally. They discover that they're an exhibit. It's apparently their future selves who are the exhibit, since they have to prevent themselves from getting captured and put into the exhibit. But the being put into the exhibit has actually already happened, and the people doing it have no access to time travel so as to be able to get them put into the past as exhibits. There's no explanation of how that's all supposed to work out, but it's the first clear instance of past-changing in Doctor Who, and therefore it goes down in history as the shark-jumping point for time travel, since that's the big evil of all time travel stories. Lots of time-changing stories can be fun, but they make no sense when it comes to the metaphysics, and this one is such a clear case of that. There are some nice, suspenseful moments in their attempt to avoid getting captured, and Vicki for the first time gets to display some of the intelligence that they had originally presented her character as having by playing a crucial role in the story, which is a shame since this is now her fifth story, and she'd mostly been relegated to getting into trouble and being saved before this point, which is what they'd mostly done for original companion and Time Lord Susan, the Doctor's own granddaughter, in the previous season, which is why she left the show). So there are redeeming aspects to the story, but the basic premise of the story was such an outrage against the viewer's intelligence that it's hard to let that affect my judgment very much.
20. The Myth Makers: The Doctor and his companions end up getting involved with the Trojan War. The Doctor is the one to suggest the horse. You get Stephen doing the obligatory fight scene that Ian got to do in the Aztecs. Not much here caught my interest. The one nice idea in the original script that caught my interest when I read about it got nixed in production. They were originally going to have Vicki be Cressida and fulfill the role Cressida plays in mythology, where she falls in love with Troilus but then runs off with Diomede (which was the role the Doctor's companion Steven had taken on), and Troilus ends up dying as a result. Running off in the TARDIS at the end would have explained the original story. But this turned out to be Vicki's final appearance, so they decided to have her stay with Troilus, which just made no sense. Plus, they didn't explain very well her motivation for this. It wasn't really long enough a stay for her to have become too attached to him. But Doctor Who did this sort of thing several times in the original run, so it's not as if this is the only instance of it.
24. The Celestial Toymaker: Only the final episode (of four) exists. This was an attempt to be intelligent, I think. It has the Doctor pitting his intelligence against a higher being of some sort, whose nature isn't really explained. I was delighted to discover that the actor playing the Toymaker was none other than a young Alfred Pennyworth from the 90s Batman movies, who I will always see as the real Alfred, as much as I liked Michael Caine's portrayal in the Christopher Nolan Batman films. I don't think the battle of wits gets shown in any way that people who wanted to see a real battle of wits would pick up on, though. Partly I'm going by what the reconstructions show, but I think you just see an unexplained board with pieces that get moved, and the Doctor eventually loses his voice so Hartnell wouldn't have to be there (a hand double is used for at least an entire episode). The scenes with Steven and Dodo were harder for me to tell what was going on than is usually the case with reconstructions, but even so I wasn't all that impressed with the story or the wacky situations they were supposed to be dealing with. Even how the Doctor resolves it didn't seem to me to be as well explained as it could have been. I know the original writer was disappointed too with how it had turned out after some rewrites, so maybe they dumbed it down in a way that removed what was originally interested about it. Either way, it was hard for me to enjoy this all that much when watching it in reconstruction.
28. The Smugglers: This was hard to follow in the reconstructions (no episodes of this one exist), because the still photos they had from on set were not very clear, and the audio isn't always sufficient to figure out what's going on. It's a pirate tale without any pirate ships, involving treasure hidden on land in a seaside village in England. It's the last First Doctor historical, and it's not a memorable one. Even the tenuous connection with the Eleventh Doctor episode The Curse of the Black Spot, which is sort of a prequel to this, didn't help catch my interest much. That story just explains where the pirate captain disappeared to, and this story deals with what happens to the pirates who didn't disappear with him looking for where his treasure might be. This might be my least favorite historical. Certainly my least favorite First Doctor historical.