Are you asking about companies that build machines just for audio. I imagine the demand isn't that high so it's going to be a high premium. I could be wrong but I imagine the needs of a musician wouldn't be so far off from a hardcore gamer, i.e. fast CPU, drives, lots of memory, etc. In essence you want the fanciest parts you can get for your money.
I think the biggest operating and performance differences you'd see would be with your choice of OS and software. Windows 98 was a nightmare for me. Windows 2000 was pretty solid but I got curious about XP. XP fixed some issues with hardware compatibility but I feel like there is a lot more software bloat going on becase my very same system feel and reacts slower. But then again I am trying to run a new OS on my relatively old PIII 450x2. Time to turn this into a server or development machine and get a racehorse for production.
AFAIK Newegg has a pretty good track record and gets high marks from geek and gear heads. They have low prices because they don't really offer support. You pretty much have to know what you want and how to use it. Good luck.