A number of judicial nominees. Miguel “I have no opinion on any past Supreme Court cases because I wasn’t there at the time and didn’t read the briefs” Estrada comes to mind, as does Harriet Miers. Or, to the extent you can counter a list of failed nominations with a list of successful nominations, I’d say that the Senate did not allow Bush the leeway to effectuate as broad a scope of judicial nominations as he wanted, both in terms of absolute numbers and in terms of consistent judicial philosophy. Bush wanted to emulate Reagan by seeding the lower federal courts with judges who would thoroughly reshape the judicial activist excesses of past years (we can argue about the definition of activism and whatever, but I think I’m accurately characterizing his perspective). I don’t think he was able to do that.
On a similar note, the Supreme Court blunted Bush’s policy initiatives a number of times: regarding Guantanamo and affirmative action, among other things.
And of course there were all those investigations and inquiries. Gonzales, Libby, Gale Norton, GAO reports about impropriety in the administrative agencies…even if these (and other similar) things didn’t specifically neutralize a specific Bush administration policy, it’s fair to say that they blunted future initiatives.
…Of course, on reflection, I see that you limit your question to Congress. So: judicial nominations and (kinda) the GAO is my response.