I hope you didn't overlook my post just above yours. Also, Neuro Hunter
over at Gamersgate seems to be right up your alley too. Never tried that, but a few guys around here were commending it. Again, it's another RPG that seems to want to be like System Shock.
Also, do you consider post apoc car combat to be sci-fi?
Didn't overlook it, just trying to keep up with the suggestions and that one deserved some research (never heard of it before). Not too sure about it. It definitely meets the sci-fi requirement, but it doesn't really seem to be a RPG, more of a hybrid shooter/resource collection game. I'm not sure those are really the two great tastes that go great together, if you know what I mean.
Already have Neuro Hunter, totally forgot I had it until you posted, which should tell you how good it actually is.
EDIT - Shadowrun is definitely one to consider (the old-school console one, not the newer travesty). I played on the Sega Genesis back in the day, but I understand the SNES version might actually be better.