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I know of only two incarnations. One was TSR's second attempt, by repackaging the Marvel Super-Heroes RPG using the SAGA card-based RPG system. The other was the most recently discontinued RPG put out by Marvel themselves.
There's also the new Heroclix Marvel Superheroes game, though I don't know how much actual "roleplaying" that involves. Probably wouldn't be too tough to make it a miniature-based RPG, though.
It was published by Marvel Entertainment early last year. Had a couple of supplements, then was abandoned. You can find exampled of play at the link above.
Hello Twilight, I have heard a lot of good things about Green Ronin's Mutants & Masterminds. It isn't "Marvel" but it should allow you to recreate any hero archetype that you can think of.
Actually, TW if you kept in contact with we the players....you would know I have an adaptation of Marvel for D20 modern....hehehe....i love my p2p program.....
Use Mutants and Masterminds for the rules. You can probably find online M&M character sheets that other people have developed for the most popular Marvel characters. Use Heroclix for the minitatures.