The Dark Knight Rises (although Batman Forever is a close second).
I love TDKR; as good as both Batman Begins and The Dark Knight are, I honestly feel like TDKR takes most of the things that were great about those films and just ups the game with Bane, Selina, and Talia and bringing the League of Shadows.
I'm inclined to agree with this. I never got the hate for TDKR, I thought it was easily the most entertaining of the three Nolan Batmans. I loved begins, but even though TDK is good, I think it's terribly overrated.
For me it's
TDKR
BB
TDK
89
BR
BF
B&R