Eyeball and copy cloning. Most of the detail is hand done, though I do use the topography tool to raise panels up when I start in some places.
Generally, I use pictures of engines, machinery, current ships (studio models), as well as my own concepts, finished models and such to make the texture set.
When I do an area, this is how i begin. I start with a base color, a few points off from an area around the area im doing...panels rarely match in color, and the ever so slight patchwork coloring adds to the realism. I then use the lasso and normal box selection tool to select my desired panels, increase the brightness of the color about 10 points and delete, creating the panel base. I do it again for a third stage panel if I want one.
Next is either adding shadow and highlight myself (15 points lower and higher for the lines, one thick) or the topography tool. Now I use the multi-tool set to lightness down, with different sizes and densities to add shadowing, concentrating on the base area and edges of the panels.
When shadows are applied, I then add lines. I use colors about 10 points lighter or darker than the surrounding panel to create the line details on the panels, having the lines get stronger or weaker in certain areas (due to lightness variations from the lightness tool) which again adds to realism. Finally comes the little light specs on the edges of the panels...not a very good weathering method, but at least its something.
I still have a long way to go though lol. Here's a pic of how the ship looks at the moment.