From what I have seen theres hundreds of color combinations for the pupa. I want to say that it depends on where your fishing. I think that if you have olive, gray, tan, and a darker color like maybe black or brown you should be covered. Ive been experimenting with different thorax cominations trying different color dubbings and sometimes peacock herl, cdc, etc.
This site is pretty good for some ideas
http://www.trout-streams.com/Tied%20Fly%20pic/Caddis%20Pupa%20-%20Emerger/caddis_pupa%20Page.htm