In no particular order

1) Incredibles
2) Hulk
3) Batman: Mask of the Phantasm
4) Spider-Man 2
5) TMNT


Nothing really needs to be said about the Incredibles, it's just that good. Loved the commentary about mediocrity in the world.

As for Hulk, people shit on this movie because it wasn't what they wanted it to be. Fuck all that, though. Hulk was the most ambitious and thoughtful super-hero flick that I've ever seen.
It wasn't afraid of its comic origins like the X-Men franchise. Instead it embraced them and proved you can still be a comic adaption and treat the material seriously.

Mask of the Phantasm: I will stand by it to the day I die, the best version of Batman in any form of media was the Animated Series. He's not even as good in JLU as he was during his '90s show. With that said, Mask of the Phantasm easily trumps all his live action movies.

Spider-Man 2 gets props because it was literally a comic on screen. While X-Men 2 felt like "the sequel to X-Men", SM2 felt like "the continuing adventures of Spider-Man" and being that it's derived from serial story-telling roots, I think it fits. Add in the subway battle, which ties with Blade 2's finale as the greatest comic movie fight scene, and you just have a great film.

TMNT - Darker than any X-Men flick. Only weakness was the Casey Jones bullshit. Y'all know you get hyped everytime you see Splinter stare down Shredder.