I usually wing it too, more or less. Though I do have a tendency to start with a shape I like and turn that into a ship. The point on centered [overall] thrust vectors is an important one; a ship with engines all on top doesn't make a ton of sense. But I'm not opposed to spreading engines around, so long as their size-weighted average location is somewhere near the centerline. Finally, asymmetry is great if you can make it work and make it balanced; top-to-bottom, left-to-right, whatever; there should be approximately equal volume on each side of a potential symmetry axis, even if the ship itself is not symmetrical. There are one or two exceptions in stock Freespace ships (the Orion, but only for its engines; it's centered roughly by volume already). All general rules of thumb, of course, but I find them helpful.
