I've had Warmoth and Musikraft, predominantly Warmoth. Never had a problem with anything I've gotten from Warmoth, new or used. I currently have 6 full Warmoth builds and will hopefully be finishing number 7 tonight I've also done 7 other builds for other people using Warmoth necks and bodies. They are all great, or at least as great as I can make them. I have had a Musikraft neck in the past and it was as good as what I have gotten from Warmoth. I think they are all quality vendors with equal quality products. For me this decision comes down to customer service. Warmoth has the easiest spec and order process, and off the shelf ordering, out of all of them. I've never had a problem with them, so thats where the limits of my knowledge leave us...
If you want something specifically charvel or "franky" or whatever I think the Musikraft and USACG might hit those marks closer than the standard options Warmoth offers (i.e. hockey stick/banana headstocks, or features specific to EVH replicas and the like).