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I'll only rank live actions films, but if there's some animated Marvel movie you like (lolololol), by all means, throw it in.
I've not seen a whole lot of Marvel's 1970's/1980's output (for example, the 1978 Doctor Strange television movie, or the 1978 Captain America, or the 1990 Captain America, or the 1989 Punisher, or - well, you get it), but I'll rank all the films I've seen.
1. X2 (2003)
2. Spider-Man 2 (2004)
3. X-Men (2000)
4. Spider-Man (2002)
5. Punisher: War Zone (2008)
6. The Punisher (2004)
7. Daredevil (2003)
8. The Amazing Spider-Man (2012)
9. Man-Thing (2005)
10. The Wolverine (2013)
11. Generation X (1996)
12. X-Men: The Last Stand (2006)
13. Fantastic Four (2005)
14. Spider-Man 3 (2007)
15. Fantastic Four: Rise of the Silver Surfer (2007)