Ironseed is alot like this. Combat and travel do take place in 3 dimensions, though perhaps not like you're looking for. The combat sequences are carried out from the ship's combat station (with systems, battlefield view, and navigation controls) rather than a more flight-sim type first-person perspective. And while the star systems are plotted on 3 axes, travel is accomplished through menu selections. Unfortunately, the game as released was very buggy - though it was later picked up by a fan group and a good deal of the original problems have been patched (available on the linked site) so the game is at least completable.