As someone said, Anachronox, although I think it's crap, especially side quests, although the voice acting is fun.
Space 1889 or whatever it was called. Although technically maybe more like steam punk, bordering on it.
Arcanum, crap again, but steam punk-ish.
Shadowrun on SNES and Genesis. Haven't played that in over a decade, forget how much RPG it is. Looks like they made a new version of it a few years back, except now it's a shitty FPS. Well, probably shitty, screen shots don't look so bad.
Centauri Alliance. Pure sci-fi, has psychic powers substituting for magic sort of.
MegaTraveller series.
2400 A.D. Not sure if it was ever released on PC. Apple II if nothing else.
B.A.T. 1 and 2. Not the most RPG'y that I remember though.
Alpha Broccoli could be called a sci-fi if you look at some of the tech. Again though, RPG qualities are questionable.
Starflight I and II. Not really RPG's, but you do have a large-ish crew with skills they can improve, lots of exploration, fun dialogue etc.
Neocron. Never played it more than 5 minutes. Think I had some trouble installing it or something, and seemed like an even crappier Anachronox. Dunno.
KoTOR I and II. Well atleast there are stats. Exploration, or point of it is pretty much non existant.
Superhero League of Hoboken. Technically post apoc, but not in a Fallout way by any means.