1. The Dark Knight - even though I thought the Two-Face ending went too over the top, the moral questions and dilemmas at the core of this film were remarkable.
2. Superman 2 - I am putting it here for nostalgia mostly. The battle between Superman and Zod + his allies on the streets of Manhattan was amazing considering the limitations of computer generated effects at the time. A great twist at the end with Superman counting on Luthor's deception to win the day. So many great moments, my favorite being the "revenge" fight in the diner at the end.
3. Spiderman - This re-launched the Comic Book movie craze and made it clear that dark and serious were perfectly fine for this type of film. The bad guy got killed at the end... literally a stake driven through his heart. That's dark!
4. Avengers - Totally different than the above because it is less serious but also more fun. The best humor of any comic book movie by a mile!
5. X-men 2 - So rare for a sequel to be better than an original, but I just loved some of the mystery and morality at the core of this film. The ending was unflinching with Jean sacrificing herself (have to pretend like you have no idea Phoenix exists).
6. Spiderman 2 - Almost reaches the heights of the original. The train battle is incredible. The concept of the arms controlling Octavious' mind was great.
7. Iron Man - The first half was amazing, probably the best origins story in any comic book movie.
8. Batman - The Timothy Burton version. "Have you ever danced with the devil in the pale moonlight?"
9. X-men: First Class - I am probably in the minority, but I thought this was a fabulous film and loved the way it integrated historical elements into the story.
10. Batman Begins - Loved most of it, but the final 1/4 really broke down for me when Ra's al Ghul returned.