I think my favorites have all been mentioned.
I used to love Alpha Centauri, Tie Fighter and Wing Commander. I'm in the process of moving flats and while packing boxes I found my Wing Commander IV box. Oh, the nostalgia.
Regarding more current games I love the Mass Effect trilogy, I really enjoyed Deus Ex: HR, I loved Bioshock: Infinite (which isn't set in the future but is still science fiction) and despite all its flaws I enjoyed the concept behind Remember Me.