I'm a huge Marvel fan so the Spiderman and XMen movies finish at the top. This is a rare case of the sequal being better in both franchises, mainly because the Goblin was cheesy in Spiderman 1, even though I loved seeing Peter develop his powers. XMen 2 wins just because it had a lot more action and less setup.
The Batman movies come next. My favorite DC character. Batman beats Batman Begins because you can't top Nicholson's Joker. It was also a big too long. I think I liked the origin of Batman in the first movie better too.
Superman 2 is a cool movie and I didn't want to leave it off.
PS I don't count Sin City as a superhero movie, though somebody else listed it. It is one of my favorite recent movies, though.
PPS Unbreakable was dope, but too different to compare to the other movies. Similarly, I loved the Blade movies, but they're so different that it's hard to include them. And if we're including Blade, we should throw The Crow in the mix too... But I think they're too dark and bloody to be in the same mix with Spiderman, X-Men, Batman, Superman, etc.