Tough to list. To me, 'science fiction' is a pretty broad genre. I mean...how does one compare futurama with black mirror?
Anyhow...here's my list, with honorable mentions that can replace the list at any time...
1. Firefly: forget star wars: THIS is how you do space misfits. Great episodes, even better dialogues.
2. 3% : the pitch might make it look a bit like "battle royale" (only 3% of the population is selected to live on "the island"), but this Brazilian series is incredibly smart and original. Easily the best thing I've seen on netflix
3. Black mirror: I'm often not in the mood for the horror it represent, and some episodes are just "meh". But some get right under your skin and shakes you up because it is so recognizable
4. Westworld: it took me a while to get "in" this world, but the amazing acting and the beautiful scenery makes it worth it to untangle the complex storylines
5. Babylon 5: the only old (and thus sometimes cheesy/outdated/naive) serie I can fathom. There's something about the diplomacy that's in it that compels me more than pretty much all other space operas that boil down to shooting aliens
Runners-up:
x. Futurama: yeah...I guess this one doesn't need introduction.
x. Cowboy Bebop: this one was a slow boil. At first I didn't get why others where so enthusiast about it, and assumed it would get better (more action-filled). It didn't...but my expectations shifted. There's just...
something...about this show that kept me coming back to it.
x. Altered carbon: the first episodes were all absolutely top notch. It didn't manage to keep the quality until the end IMHO, but still: it's worth watching.
x. X-files: haven't seen an episode in ten or fifteen years, but...yeah. Keep in mind: X-files was not just "a great science fiction series". It was 'a great serie'. Other series of the time were almost all sitcoms or clearly below the quality of movies. X-files's influence was one of the main factors that ultimately gave movies a run for their money.