I've been thinking about what would make a great sci-fi horror RPG and I even had a stab at creating my own called Those Dark Places (the playtest version is available on my website http://www.farsightgames.com/) but now that I think of it I might as well stick to the tried and tested system for horror - Call of Cthulhu.
All you'd need is rules for spaceships and what that entails and you're done. The sanity rules are there, the system is there, it's all there. In fact, it wouldn't surprise me if Basic Roleplaying, the generic RPG using the same system, already has tons of rules in there for spacefaring games.
I should have thought of all this before I started to mess about with Those Dark Places. Dick.