Version 3- Now with revised palette. As stated before, try to use it, and if you add some put the colours in the SPECIAL section. If you make a component separately please include a palette so I can integrate it. Anyway the palette is divided into sections.
Colours: For a splash of colour. Each set has a dark, normal, light and very light version. The normal is second from the left. Use the normal for general shading.
Standard: Regular old component colours. Dark, normal, light, see above. The very bottom gray is for leads and metal.
Label: Labeling colours. The blue is for electrolytic capacitors.
Special: Special colours for special components where I just couldn't sub in a standard colour. Avoid if possible. If you add a component with a special colour put the special colour in here.
There is also a "quick palette" in most of the sections.
Credits go to me, Rekarp, and two others that I forgot. The OP should know.
OP- This is the latest revision. Please add or link to these palette instructions.
EDIT: I've got a small SMT sheet on the way. As soon as I get around to uploading it...