HERO (a.k.a. Champions) is my game of choice. I find its system is simply unsurpassed in flexibility: I have yet to come up with a PC concept I can't model in HERO. While it is complex, most of that is due to its flexibility- you can model just about anything 10 different ways- the complexity is mostly limited to character creation. Once you're playing, nearly everything you need to reference will be on your PC sheet.
Mutants & Masterminds is also exceptionally flexible, second only to HERO in this regard, IMHO. It will also be easier to understand if you're familiar with the D20 system.
While I've not played a supers game in it nor particularly care for it, GURPS is another game quite capable of modeling a huge variety of character concepts.
Besides those, I've played a variety of superheroic games over the years. While these others may not be as good as modeling the whole supers genre as the ones listed above, they may do a better job of modeling a particular subset of the genre. For example, if you really want to play in the Marvel or DC universes, the games designed for those companies' comic lines are really where you should start looking.
Do you have a particular supers campaign type in mind?