This is going to sound really esoteric but there is this game called Buck Rogers: Countdown to Doomsday that came out in 1992 and was by SSI, glad bless their souls. It was Fallout before Fallout. You had a team that you put together and you set out on your missions. There were so many side missions. A ridiculous number. The grahics weren't anything special for the tome but the game was really fleshed out. I never beat it since I got jamed up in a battle that I couldn't win and I hadn't saved in like forever. It strangely came out on the Megadrive, and was a favorite on that system, which is really weird since the game looked like something you could put out on the Nintendo if you had a carteridge with enough memory. The PC version was 8 meg, which is a shit ton if you don't have sampled sounds or decent graphics. The game was pretty bad ass. As much as Faster Than Light gets love, Bucker Rogers was 10 time better but just with old grahics. The game can be found on Abondonware or freeware sites now that it is out of copywrite. It was pretty bad ass for the time. I think the push for state of the art graphics has made it too hard or risky to do something different and deep.
Back to the ship though. The worst ship in the game to run into was this massive living ship. It looked like a centipede and you had to board it to take it out. I always loved the idea of a living ship.
My second favorite ship was the Star Forge from Star Wars. A big weaons forge that sucks off energy from a star to create fleets of ship. The ship basically took care of its self for centuries when it was abondaned with its on ship reair droids. The ship is smart enough that it is considered sentient.