I can't say much about one motherboard vendor versus another, although I would like to take a moment to gripe about generic PC parts. A few years ago, I built some then-screaming 1.3GHz AMD Athlon PCs using Gigabyte motherboards with the AMD chipset. Then they started going flakey. Turns out the chipset fan was a piece of crud and got itself stuck on occasion. Also, turns out the ECC RAM I bought refused to run at full speed without occasionally having errors. And, they were mind-numbingly loud. Those PCs are now downclocked to 1GHz and running in the lab.

Our new desktop PCs are Dells. They're whisper quiet and they just work. The fan's only go into high gear when the CPU is slammed.

If you insist on rolling your own, I'd probably recommend going the Intel route, and make sure you get one of the newer Hyperthreading CPUs. When you're running EAC or grip to import your music, you can have it run two copies of lame at once, and you should get noticable improvements in encoding throughput. Also, you might want to put serious effort into noise issues. The difference between a quiet PC and a generic PC can be stunning.

Personally, if I was doing a from-scratch PC myself, I'd get a Shuttle XPC. They're pricier than generic PCs, but they have a nifty and quiet cooling solution, and they've got all the ports you could ever want on board. All you need to add is a graphics card, hard disk, cd-rom, and memory. You can get finished systems at GamePC, or just play with their online configurator.