Here are my top 10.
Guardians of the Galaxy - just brilliant, the humour is wonderful, the characters are perfect and the story is great. All this around a cool 70s soundtrack.
Avengers Assemble - this is just an excellent story which keeps going from start to finish, action packed with some brilliant moments of humour (the Hulk puny God line is perfect).
Batman Begins - I just love this reboot, the story is excellent and I think it really captures the comic book world (the follow up movies are good but a bit too real worldy). Plus I love the fact that Batman is vulnerable, it gives these stories an extra edge. I must say, an excellent trilogy.
Deadpool - this was a surprise as I wasn't expecting big things, however it's quirky humour really delivered.
Spiderman (2002) - this movie kick started the huge trend in recent super hero movies and I loved it, less dark and more fun. Ok so the affects aren't quite up to the latest movies but the story is great and so are the characters (far better than the latest re-boot).
Iron Man - Robert Downey plays this role perfectly and I love the story (ok so the ending is not brilliant).
Watchmen - I actually love this movie. Ok so it has quite a few faults (the 70s style sex scene!), but I just love the atmosphere and the portrayal of super heroes as vulnerable, everyday people.
Incredibles - it might be animated and it might be a kids film but it is an original concept and a great story, plus the animation is also very good.
Superman (1978) - it may be old and it may be a bit dated, but it set the superhero movie standard, plus the cast is excellent.
Sin City - this is my final choice, it may be violent and a bit surreal, but the imagery is brilliant and I love the characters.
Honourable mentions to: X-Men 2, Spiderman 2, The Dark Knight Rises, Captain America: Midnight Soldier, Kick Ass and Avengers 2.