City of Heroes is now a free game. This is not a Marvel game, but the similarities made Marvel Comics file a lawsuit against years ago, but it was then settled. It's a generic superhero MMO inspired by Marvel.
Another generic superhero MMO is Champions Online, which is now free as well. Before this game was created, the developer was making a game called "Marvel Universe Online". However, for some reason, MUO got cancelled and then they made Champions Online.
Now for official Marvel games, there's Marvel Super Hero Squad Online. However, this is more kid-oriented.
Last but not least, there's an upcoming game called Marvel Heroes. This was originally known as Marvel Universe Online. It's an MMO as well, but the gameplay is more similar to Diablo.
The best one? Definitely Champions Online.