There's been a lot more on Justices Thomas and Scalia voting together, which I blogged about before. Volokh has a list of which pairs of justices vote agree the most in their endorsement of opinions. Scalia and Thomas are seventh in the list. Six other pairs of justices are more likely to agree than those two are. Four of those six pairs are more likely to be considered liberal. Two are conservative-moderate pairs (Rehnquist with O'Connor and Rehnquist with Kennedy). The most likely to agree are Souter and Ginsburg, 12% more likely to agree than Thomas and Scalia.
Will Baude has a New Republic column arguing his original point with more detailed explanation, and Volokh has more about the differences among the justices on the free speech issue. Thomas and Scalia aren't as close on free speech as the "Thomas as Scalia's house slave" narrative would have us think. A few other posts at The Volokh Conspiracy have relevant information also.
One issue I hadn't been aware of was the formalist/pragmatist division on the Court, which doesn't match up with the conservative/liberal division. Ginsburg, Souter, and Stevens join Thomas and Scalia on the formalist side, with Rehnquist, Breyer, O'Connor, and Kennedy on the pragmatist end. So when the votes split on these issues rather than conservative/liberal (or originalist/activist) lines, Thomas and Scalia will usually end up agreeing even though the other conservative and the two moderates disagree. Their similarity on those two issues explains why they're more likely to agree than either one will agree with Rehnquist. This explains why their agreement would be as high as it is, even if they do disagree more than the "Thomas as stupid lap dog" myth has it.
I was actually fairly impressed at the independence Thomas has shown in numerous cases. Almost all of the times he's disagreed with Scalia (but not all), I find myself agreeing with Thomas. Scalia is more willing to concede to precedent, even when he disagreed with the arguments for that precedent. Thomas is more insistent on going back to the original intent of the Constitution itself, sometimes by viewing other documents by the founders such as the Federalist Papers, rather than favoring an opinion that was bad to begin with just because it's been written and become part of the legal tradition. This was one of their differences in this week's cases. Thomas used the Federalist Papers to ground presidential leeway in a time of national security, and Scalia invoked precedent also from way back to argue that a president shouldn't be given such powers. In the pornography case, Thomas sided with those who found regulating internet porn to be unconstituational, while Scalia would have banned it completely. I have to say I prefer Thomas' approach on most of these cases, and I think his more favorable attitude to free speech tendencies are what bring him on the wrong side of the porn case. (I think porn isn't speech and shouldn't be protected by the 1st Amendment, and I sometimes think it's harmful enough that it should be banned even if it did count as speech. So I'm more with Scalia here.)
They disagreed over a case involving foreign courts, and Scalia sided with foreign precedent, while Thomas decided based on the issues. Baude lists a number of cases with Thomas' own additional opinions, where he qualifies or adds to Scalia's. He had to have a separate opinion beyond Scalia's in the sodomy ruling last year just to say that, while he doesn't disagree with Scalia on anything, he needed to express his disagreement with the Texas law that both Thomas and Scalia thought Texas had a right to have. If he'd been in the Texas legislature, he would have voted against the law. Still, it wasn't the Court's place to deny Texas the right to have such a law. I fully agreed when I read that, and I haven't changed my mind since.
Now I have a little more understanding of why Justice Thomas is President Bush's favorite justice. Most conservatives I've heard on the issue pick Scalia, and I was sort of deferring to their judgment in considering him my favorite, but I think I've changed my vote on this one.