USS Sulaco is everything a space ship should be to me, but i feel we are missing mentions (as far as i can see) of a few good ones.
Serenity. Obviously. I seem to recall they built it (the interior) as a single set, to enable them to do consistant shots moving around the ship.
Surely thats been mentioned above?
Icarus II from sunshine. Great space horror with some really thoughtful design behind it.