Interesting thread. I am a novice builder but cannot afford to build the number of guitars I would like. Last week I emailed every friend I have offering to build any guitar or bass they can dream up or go with a copy of something they like. My "fee" was simply that they pay for all material and $100 up to $200 for my time, depending on the complexity of the build.
It seems a lot of folks here seem to assume it is not possible to build a quality instrument without first creating large numbers of junky guitars that nobody would want. I know a lot of it depends on the skill of the person, but I feel my fee (which almost seems exhorbitant based on what I have read here) is completely justified. If I spend $500 on materials and charge $600 for the guitar, yes, you can easily go and pull an assembly line guitar off the shelf of a music store that will be just as playable, but you will not be playing a guitar you know was built just for you exactly the way you want it. I think $100 is a small fee for the uniqueness alone. Just my 2 cents.
Greg