GURPS is a very modular and customizable pencil and paper role-playing game system. GURPS stands for Generic Universal Role Playing System. It can be used to play games in a super-hero setting by using the book titled "GURPS Supers". You can get a printable PDF version of the "lite" rulebook for free at http://www.sjgames.com/gurps/lite/.
Several advocates of other role playing systems feel GURPS Supers is best used for Heroic games, but is lacking in modeling comic stories which are part of super-heroic games.