Classic Traveller will always be my first love...but I have tried a few others....
Prime Directive-- This is a Star Trek game put out by the same people who do Star Fleet Battles (which rocks btw) and is set in that universe...strictly old series stuff. You don't play ship captains or anything like that...the players make up a Prime Team assigned to the ship (picture S.E.A.L.S. also trained in science, linguistics, diplomacy etc...) They're a specialist landing party designed to go where the ship can't and do the things the normal crew can't do. It's very well written and the rules are easy to manage.
Champions-- Yes it's a superhero game, but the Hero System is very open and cutomizable to any genre (if memory serves it's what Steve Jackson originally ripped off to form Gurps, but don't quote me). Our group did various Sci-Fi games with it...ranging from Superhero's in Space to Classic Space Opera. Works well.
Gurps-- I won't touch it pretty much for personal reasons. I know people in the game industry, some who have written some major suppliment for SJG and know of Steve's habit of 'appropriating' ideas...our circle calls gurps the Generic Underhanded Roleplaying Pilfering System, but I'm not bitter
I know some are already collecting torches and pitchforks for me, but I do want to mention one product that really frosted me. Behind the Claw. I will admit it's a great guide detailing EVERY planet in the Spinward Marches...but did you notice that in the descriptions they tell the secrets and give the endings away for the Traveller modules, aka their competitors? 'So that's the secret behind twilight's peak...guess I don't need to run that...I should probably go buy a gurps module instead...yeah, right.'
Again, forgive the small tirade, but let's move on
Star Wars-- I am also a fan of the WEG version. We found it easy to use and mountains of source material. I haven't played it for a while, but I remember no complaints with it. We had fun playing it, which is all that really matters.