Spider-Man 2 is great, most of the other 3D Spider-Man games pre-Spider-Man 3 are pretty fun too. The Marvel Ultimate Alliances/X-Men Legends are also good, although they don't give you the feeling of being a superhero like Batman and Spider-Man do
also Freedom Force. Freedom Force is the best, despite not being based on actual comic characters.
-- For your BlAcK TuRtLe. At least Kupo has class and doesn't MESSAGE the people -Dr Pizza
And the X-Men Arcade! ...Might not hold up as well today, but sooooo good in the past. Also really enjoyed Spider-man for PSX/N64. All those costumes and collectibles.
Hulk: Ultimate Destruction, the two PS1 Spiderman games, and depending on how masochistic you are, one of the Batman games from the 16-bit era: you have the SNES game, which is easy but kinda slow and the Genesis game that is murder but has some amazing music and makes you feel like a boss when you make progress with it.
Also, Spiderman: The Arcade Game, which is another fun one.
--
Currently playing: League of Legends, Chrono Cross. Current Projects: Fool's Overture, CYOA: http://www.gamefaqs.com/boards/8-gamefaqs-contests/60143513
The first Batman on NES is good, and I actually like Silver Surfer NES as well
Stay away from almost every other NES superhero game though
If we're including Arcade games, The Punisher is my favorite beat-em-up of all time and probably 3rd favorite arcade game of all time, and if you get 4-6 people on it the X-Men arcade game is fun too, but that one can get super boring and repetitive if you're playing by yourself or only with 1 or 2 others
hulk ultimate destruction is one of my personal favourites. You can pick up random pedestrians, climb to the highest point in the city and punt them as far as the hulk can punt.
Hulk Ultimate Destruction is a favorite of mine aswell.
Unlike most Hulk games, it actually makes you feel like the Hulk running around smashing ****. A good superhero game is a game that manages to make you feel like you're actually playing the super hero( Aside from the obvious requirement of actually being good). Which is why games like Spiderman 2 shine so well cause the web swinging in that game is unmatched.