Tonight I picked up Arkham Asylum and Wolverine. Both are awesome and well done games License or not. The only other awesome super hero games I can think of are Death and return of superman on the SNES. Spiderman and Venom Speration anxiety and Batman on the PC Engine. Not counting fighting games here either since everyone knows the VS games are awesome.
Batman Returns on SNES, Batman on NES, the X-Men arcade game, Spider-Man on PS1...and of course, there's Lego Batman.
The Ultraman fighter for the Saturn is a real gem. Any Capcom VS. game sucks ass compared to this programmed brilliance. Seriously though, I think the Cel-Shading Superman game on the first Xbox wasn't too bad, same with the newer Spiderman games on Xbox-
I remember enjoying Spider-man 2 (swinging around the city was so fun). I doubt it holds up now though, and it's nothing (quality wise) compared to Batman: Arkham Asylum for sure.
Spiderman 2 on the Xbox was amazing at the time, sure it had some repetitive-ness (omg a little girls balloon is flying away), but the main meat of the game was great, and the swinging unmatched.
X-Men 1&2 on Sega Genesis. Atleast the first one I liked and thought was pretty good. X-Men Mutant Apocalypse on SNES was a good game as well. Spiderman & Venom Sep is very similar to Maximum Carnage the Spiderman game. Batman on the NES is definitely a must play for super hero games. Other than the games I mentioned I can't think of anything else that stood out to me as a good game. There are plenty of super hero games to avoid though... Plenty of shitty Batman, Superman, and Spiderman games. Even X-Men on the NES is a pile of shit. Wolverine on the NES some people hate but I actually think it's decent.
Superhero games are my guilty pleasure, theres actually a few good ones if your willing to keep expectations at a certain level. For current gen graphics, I recommend Spiderman 3 or Spiderman Web of Shadows. Free roam spiderman games that are pretty decent. Spidy 3 had some naysayers but for the price you can get it at now, its worth it. The Xmen Legends series and Marvel Ultimate Alliance, action rpgs with marvel characters. Tons of extras like bonus missions based on famous comic stories. Nuff said! The first xmen game on the genesis is a classic.