For the most part, I like big bold shapes, so I try to find uniqueness in mixing various shapes together. IMO, the best spaceships are the ones that can easily be described, like the tie fighter is a flying H, or the death star is a sphere with a giant crater.
I usually start with a function the ship needs to have, which suggests certain shapes. I then start playing around while sketching until some combination of those shapes looks interesting. Once I have that, I ask if a vehicle this shape makes sense with what the ship is trying to do, and do some editing based on that answer. Then the rest is adding medium and small details to compliment the larger shapes.
You can do this with sketching, or in a simple 3d application, lots of different ways. Good luck!