The problem with most computer companies that allow you to "custom build" your computer is they give you choices within a range and never disclose much product information. Many are still building 64bit and dual core systems on 180Watt power supplies.
You get to pick between a 80GB and a 250GB HDD, but they dont tell you if it's a Seagate Barracuda or a JinkyJoo HighWhine. You don't know if it's got a gig of Micron based memory or PowMem chips on a Waffle wafer.
Building your own, when able, is always the best way to get quality, name-brand components. Otherwise, a company that discloses it's brands or is known for quality builds is good.
The major household brands, Dell, Gateway, HP, Compaq, etc, are all made in the same factories overseas, and though the build specs may differ slightly, they pretty much all use the same parts. Quality is not about high numbers, it's about manufacturers specifications and how they stand behind their product.
If you are not a system builder with access to wholesale distributors, NewEgg is one of the best sources out there.
Best.
I'm sorry, my answers are limited. You must ask the right question.