Mayfair Games' Underground had one of the coolest dystopic superhero settings I've ever seen- in an RPG of comic book.
SPI's Universe was a sci-fi game that could have been a real contender against Traveller, but the company went under before the first supplement could be released. As I recall, it had some sweet planetary system generation rules, and it used RW physics for space combat...
RIFTS. Yeah- I know how popular it is/was. If it had had better mechanics and playtesting, it could have been HUGE. Every campaign I participated in, either as a player or GM, was completely cool...but mechanics and obviously broken sections eventually wore people down.