Right now? My ranking is:
1) Mongoose Traveller - simply because of the versatility, widespread support and multiple settings covering a full spectrum of styles from space opera to hard sci-fi to gonzo (my unabashed favourite is Judge Dredd I have to say). I love some of the subsystems. You can still use most of the Classic and MegaTraveller material too. It may also get a boost whenever their Prime Directive (Star Trek) book comes out. Avoid T5.
2) Star Wars - Edge of Empire. Early days, obviously, but everybody knows what it is about and if your group is prepared to buy into it, the dice system is fun. It's richly themed setting offers years of entertainment. And there's a lot more still to come out.
3) Doctor Who - Adventures in Time and Space - Really easy system and a lot more flexible for running a variety of scenarios than you might think. I ran a successful Unknown Armies scenario with it the other day, and it was a blast. The best thing is you can take a completely disparate bunch of sources for inspiration and they'll all fit in with the broader premise seamlessly. The de-emphasis of violent combat really brings more thoughtful play. Well supported too, including the alternative Primeval and upcoming Rocket Age games.
4) Warhammer 40KRP - Five different games in the same (vast) setting. If you dig the dark, gothic elements again it's a richly themed set of games. Percentile based, which isn't everybody's taste apparently, but pretty straightforward nevertheless. My favourite is probably Deathwatch, as I like the Marines, but each game is distinct in gameplay.
5) Shadowrun - The most enduring Cyberpunk game is as well supported as it ever was. The fantasy elements might grate but it's pretty obvious what they are before you begin play. Cyberpunk 2020 and other editions have long since died.
6) Eclipse Phase - Transhumanism hard sci-fi, mainly for those who like Shadowrun's style but want something with a little more verisimilitude. Other games, like Nova Praxis or the older Transhuman Space are similar (but not quite the same) if you prefer a non percentile system. Eclipse Phase seems the best supported currently though. Not sure about the politics involved in Transhumanism though..
7) Paranoia - Maybe not for long term gaming, but perfect for one shots. Can be played straight or slapstick and still drives home an evening's entertainment either way. Very clever game.
8) Call of Cthulhu - Versatile enough to embrace sci-fi wholeheartedly. The aliens are all pretty exotic still, and can form the premise for a Promethean/Alien series of starship encounters. In the modern day, Delta Green and The Laundry are a perfect fusion of spy thriller and sci-fi horror. BRP is actually a very good fit for hard sci-fi.
9) GURPS, HERO, Savage Worlds and FATE all have various settings to support their systems. Some of them are pretty good/amazing depending upon your loyalty to those systems.
10) Blue Planet/Fading Suns - fan favourites from the 90s, still lovingly kept in print by FASA. Certainly interesting enough to try out though.
