Unlike heroic fantasy, there isn't one big sci fi games.
At the moment, I see mostly people playing Alien and Coriolis. I played only a couple of one shots, so have no strong opinion on them. But Alien's tension mechanic is neat.
Eclipse phase has an amazing lore, However, the system sucks, if you like the lore get the FATE of the eclipse version, not even that FATE is great, but it's a functional system unlike the D100 one