As a massive Superhero and comic book fan. Its really difficult to choose between many of these. X2 and Spider-Man 2 has always been some of my favorites due to Spidey being my favorite superhero and X-Men being my favorite superhero team. I always love Burton's Batman, especially Batman Returns. Christopher Nolan is overrated, he did a good job but I definitely prefer the style of Marvel films. I really enjoyed The Avengers and think Thor is pretty underrated. DC does best in the animation department.
I'm surprised there is no Hellboy or Hellboy II! Those are some of the best IMO.