Well, the first thing I generally try to do is increase the contrast a little in an effort to make the distinct sections of the ship stand out better. The Curves adjustment in Photoshop works well for this, as does a generic sharpen filter with low settings. Then, I try to make the colors a little more uniform based on area, so that it has a more sprite-ish feel to it, instead of the smooth and blended feel from the original render. For example, I'd create new layer, sample a color or two for the wing of a ship, and color that wing in with that color only. I'd then drop that layer's opacity to about 60%-50% so there's a little variation, but not too much. Next, I create a new layer with the mode multiply, and with a 1px brush, begin painting in all the details--hull plating, little doodads, etc--everything done here is usually pretty sharp and stands out, which really makes it look more like a sprite than a render. Finally, I add in the lights and other glowing portions, and do any other corrections that need to be done. If you're working with an Ambient Occlusion layer, make sure it's at the top of the layer stack, otherwise it'll get drowned out by everything else. Positioning it right below the multiply/detail layer works too.
Original model:
Base render with AO:
With contrast/filters:
With painting: (Didn't do it real heavily here, though, as it didn't need it)
With detail layer:
Final, with lights: