I have fished a small river system for many years and found that color doesn't matter too much. I have mainly used the Yum Crawbug in black neon, green pumpkin Texas red, and crawfish (watermelon and orange).
What I have found makes a huge difference is size. The larger Crawbug will catch a fish or two once in a while, while the little Crawbug has gotten crushed. Same goes for the pit boss jr vs the standard version. So it appears that matching the size of the craws is very important, and having seen some on my system, the smaller baits match the real thing the best.
Crawfish scent helps out too
I have read this before and have tried to fish crawbugs, Berkley craws, etc with one of the claws bit off and have never gotten a bite. But put a new bait back on and I am back on the fish. I mostly fish for smallies, and maybe they like to tear apart a craw on their own vs one that is already injured? Smallies definately have an attitude problem, so it wouldn't surprise me.