I use a method similar to Atrocities’ with heavy emphasis on the ACDSee. Where it differs though, is that I’ve found how to pack much more details into the minis. Instead of drawing them in the 36x36 space, I use the portrait size 128x128. I can put tons of detail into the ship that way.
Another method I use is to take a texture from the portrait to get a base hull color. I fill a 36x36 square with it with some variations so it has a random look about it. Then I take another 36x36 in black with the outline of the ship cut out, and drag and drop over the texture square, and you have an instant ship! All that is left to do is add details to it.
Finally, to take away the “hard edged” look the minis might have, I resize it through ACDSee a few times, and it softens and blends the colors to give it a better (I think) look. When you do this just remember to fill the black with a contrasting color to take out the ‘halo’ around the ship that will be visible in nebulas, and if its bad enough in the system and combat windows.
Hope this helps!