I have only ordered from Guitarfetish once, and the order only came just today. I ordered some single coil pickups and I have decided to try them out. So the jury is still out on them.
Never purchased from GuitarpartsUSA so I really can't say.
I have ordered from StewMac, and they appear to be a quality outfit. They are somewhat on the pricey side, some of the stuff is expensive but they also seem to carry things that nobody else does.
Another outfit that you may, or may not, have heard of is AllParts(
http://www.allparts.com). They also have a great selection of tools and parts. I have never ordered from them however so I can't make an opinion if they are good or bad.
Another outfit is Warmoth(
http://www.warmoth.com). This outfit actually makes guitar bodies and necks for sale. They always have a running inventory of necks and bodies available for sale. I have ordered things from them previously and the service and quality are excellent. You can even order necks and bodies made to your own specs. However, this outfit is pricey, an unfinished neck (no frets, no finish, no nut) will be about $200.00 give alot or take a little. Prices vary on the necks by the types of woods used. Some unfinished necks with exotic woods can be as high as $900.00 unfinished. They have finished necks too-same pricing applies, it depends on the type of woods used. Bare minimum for a finished neck would likely be around $300.00 but I have seen one or two made of highly exotic or figured woods as much as $1000.00. The majority are strat or tele necks but there are others. The quality is excellent however.
They also keep a running stock of finished and unfinished bodies. Again, price depends on the types of woods used and the type of finish put on the body. You could get an unfinished body of basswood or poplar for $190 give or take, or an Ash body for $210-$250, make it an Alder body with a quilted/flamed maple top or figured Koa wood and the price can be as high as $500. If a finished body is what you want bare minimum that you could expect to pay is about $250.00. They also carry everything else you would need pickups, pots, wire, pickguards, knobs, bridges, tremolos etc... On some things pricing is competitive with other outfits and on some things the price is higher. Again the majority of inventory is in strat or tele style bodies but others are available.
Another option is to go hunting on Ebay, there are a host of shops that put all types of guitar parts up for sale. Mainly it is pre-finished bodies and necks. I peruse those forums a great deal and I must confess that I don't see too many auctions for uncut bodywood. I know on Ebay it is "buyer beware" but I have made a number of purchases that I have been quite happy with. Its always an option.
Hope this helps.