#1 - D100 "Classic" Marvel Super Heroes - The extensive amount of product that was released for this system combined with a simple and flexible rules system brings to life Superhero RPGs and the Marvel Universe like no other. Still beloved by fans today.
#2 - Marvel Universe Roleplaying Game ("Energy Stones") - Using resource allocation instead of dice, this game sold well but wasn't supported by Marvel and ultimately failed to impress fans.
#3 - Saga System (Marvel Super Heroes Adventure Game) - Deeply flawed and rejected by fans, this card-based system caused fans to balk by the droves. Simply the least liked Marvel RPG.
The Marvel Universe remains an amazing place to roleplay. Since there are is no current system to turn to, I strongly suggest you check out the Marvel D100 roleplaying game. You can still get it cheap on ebay (or perhaps BitTorrent if you want an illegal download).
One has to wonder how the RPG scene has gone since 2004 without a Marvel RPG. Certainly this void shall be filled soon, considering that DC just released core rules using the Mutants and Masterminds engine.
But whatever the new RPG is, it had better be darn good (using the D100 system again would be a nice start!) or fans will stick with what they like - Classic Marvel Roleplaying.