For example, the greatest RPG campaign I ever played in was with Palladium's Robotech RPG (technically we were using the Sentinels rulebook, although the GM had all of them).
But after years of consideration I'm convinced, as is often the case, that the campaign's success lay in the GM, not the rules.
Or I could go with the Star Trek RPG from FASA.
When I went from elementary school in 7th grade to high school in 8th (which is what happened in that particular region), I went from playing D&D with one other guy to having access to a much larger gaming community of older people, and they were playing Star Trek. It was my first real experience with a gaming group, and my first campaign with a GM who was an adult. It was a whole new experience, and I have a lot of sentimentality for a game that had a lot of issues.
But no, hands down my favorite sci-fi RPG is (to the surprise of none who read this blog regularly) the Star Wars RPG, Second Edition, from West End Games.
This game captured so well not just the space-operatic innocence of the original trilogy, but also in general how players wanted to gallivant around in the Star Wars universe. Was the game perfect? No. There were serious issues regarding game balance between PC's (if you were into that sort of thing), and years later I would read on RPG forums about how to break the system using Dark Side points, one of the many reasons why I don't bother going on those things any more.
There's lots of other great sci-fi RPG's out there, but this one is just plain fun and has aged very well.