For me, my ranking would be this
1. Spider-Man 2 - Simply, the best a super-hero movie has gotten. While it can be cheesy at certain parts, it feels appropriate and each characters serves a major purpose to the storyline. While I still have a problem with the way MJ has been translated (she comes off too much like a man-hoppin ****e), the character overall has a FIRM place and reason for being there.
2. X2 - Its not the best in story, but definitely the best TO THIS DAY, for being a pure kick-ass movie. If you want a movie to have a good story, and a true testosterone-amped super-hero flick, this is the movie for you. Only flaw? Too much to cram sometimes and Cyclops plays virtually no role which leads to his uber short screen time in X3
3. Superman/Superman II - To me they're both on par and they're pretty much one big story. C'mon, this movie deserves a higher place on ANY person's super-hero category. This is the movie that not only gave birth to the super-hero flicks - but serves as a template for ALL super-hero movies. Almost every major comic movie that has transpired borrows/pays homage to these two movies - Superman I in particular. Just look at it. The beginning credit sequence forced other comic movies to have creative openings. The whole montage of saving other helpless victims. The farewell Superman Scene as he flies into space at the end is imitated with Batman's standing presence (and Catwoman's in BR), and Spider-Man's city swinging. Superman had a great cast for its time, and was made with dignity and respect. *Yes even some Lester parts in II was better than what Donner originally had in mind* Oh yeah and I forgot. The best super-hero score to DATE.
4. Batman Begins - I think this movie is highly overrated. There are some serious editing issues (and no I don't care that its intentional), and I'm sorry, but Katie Holmes' character was such a throwaway. Still, Begins is an awesome movie. Bale is THE best choice for Batman. Michael Caine as Alfred is brilliant. Morgan Freeman in a Batman film?! COOL! Pretty awesome story, and great backdrop for the character. Can't wait for Batman Returns Again. Liev Schreiber for Harvey Dent damnit!
5. Batman Returns - While highly stylized, this movie took a more story approach than its predecessor. Catwoman was cool, and Penguin was entertaining. And Michael Keaton as Batman is pretty wicked.
6. X-men - Has an ok story, but the ending feels majorly anti-climactic. The movie also had a bare-bones feel to it, maybe due to its length.
7. Spider-Man - If Spider-man wasn't one of my favorite comic-book heroes, then this movie would be way lower on the list. Enjoyable flick with a good origin story. Surprisingly the duller parts are WHEN Spider-man shows up. The cheesiness feels cringe-worthy, and Green Goblin, while translated ok, still feels miscast.
8. Hulk - This is a terribly underrated movie, but at the same time not a very enjoyable super-hero film. Great on characters, great on acting, great in technical standpoints. However the translation from comics, and the story is a little weak.
9. Batman - How some have called this one of the best super-hero movie really perplexes me. This movie is PURE style - which is good, yet bad. The story is incredibly weak, yet it is awesome eye-candy. Jack Nicholson owns the scene and along with Michael Keaton, they pretty much save the movie. Oh yeah, and still to this day Kim Basinger is the BEST Batman girlfriend.
10. X3 - I actually tend to like this movie about the same as X1, however it was incredibly dissappointing. Cyke's complete shaft, Storm's bigger yet unimpactful part, the taming of Wolverine, and major editing issues hurt the movie bad. However, its got great action, SFX and Ian McKellan and Hugh Jackman are still awesome. Still don't know if I want to own it on DVD though.
And thats it. Oh and the Evil Superman vs Clark Kent deserves honorable mention. That was good enough to make me want to download Superman III. But I still refuse to own it unless I have to.