I find that I'm inspired by pens. This leads to a long, thin, graceful looking ship. The clip becomes a hooked-out bridge or launch bay, and there's a mother of a death ray mounted down the spine.
Generally, I think that the degree of aesthetics present in a ship should be proportional to the technology. Advanced ships look like glass skyscrapers or organic forms, whereas less advanced appear boxier and metallic, with a good amount of greebles.
However, I find it's most interesting when you "get dirty" and design a ship from a practical level. What is the ships function, and how should I design it so it accomplish it effectively and efficiently? Who are the inhabitants, and what are their jobs, how do they move about inside. A fighter just needs a cockpit and means of egress (unless there isn't a pilot, or the pilot is permanently integrated into the ship). How autonomous is the ship? If it's intended for long voyages, it needs berths, a rec/common/kitchen area of some sort (depending on the inhabitants).
With large ships, things become increasingly architectural. You probably need internal corridors, levels and/or compartments, and possibly lifts. You'll probablly want a nifty bridge, this should be centrally located. Does your ship have "magic" artificial gravity? If not, and if the inhabitants aren't specially adapted to zero-gee ala Shivans, large rotating sections are almost a must. These are tricky to implement structurally.
That's not to mention the mechanical aspects. What is the ships power source? Cold fusion? Antimatter? Black holes? Does it need fuel? Does it need fuel tanks? A ships power generator and propulsion unit aren't necessarily the same thing. They may not be related at all, or in different areas of the ship. Strictly speaking, if a ship has an engine exhaust, then material must necessarily get ejected, and the ship must necessarily need fuel of some form. This is probably one of the most violated rules in sci-fi: unless you make up some very exotic technology, you can't have a ship that can function and expend unlimited amounts of electric, kinetic, nuclear energy indefinitely, without requiring input of some form.
That may seem very restrictive, but introducing problems leads to more opportunities for creative solutions.
