The Dark Knight. Nolan takes everything he setup from Batman Begins and runs with it for the sequel. Acting, action and storytelling is just that much better in TDK. I don't think Bale gets as much credit in the film as he should, but his Bruce Wayne looks like a man with the world on his shoulders. Everything that happens in the movie is a reaction to what he did in the first film. It's all about escalation. Seeing his Batman match wits with the Joker and finally understanding how he has to deal with these "super criminals" that he inadvertently creates is some damn good stuff. That prewitt building scene near the climax of the film is still the best Batman scene put to film, IMO.
I could see the case for Batman Begins over it tho, because Begins is a hell of a film. But The Dark Knight is just a beast of a film. It's like Empire vs A new Hope or T2 vs T1.