I was looking down this road at one point about 6 months ago. Building a new system or buying a pre-built. The only reason I entertained the thought of buying a pre-built machine was because I am lazy, and didn't want to go through the trouble of building it. I ended up going the newegg.com route yet again, and here is why.
The system i ended up with is a 3Ghz AMD64x2 (dual-core) with 4gb of ram. For my Motherboard, Chip, ram, a new HDD, case, and videocard. I spent $720. From Dell i would have gotten a machine with one quarter of the ram, single core processor, and ony about 2ghz. Also I was going to pay double to tripple the amount i ended up paying. I run Vista x64 with an e-mu0404, and can normally keep my latencey down around 5, the highest I have had to go was 8. I use reason rewired into sonar quite a bit /w tons of VST's running, and this machine never chokes on me. The only bottle kneck I have now is
the e-mu0404 but thats a whole other thread in of it's self.
Build the machine on your own. You will get more out of it, and be able to put more into it. Plus you'll save a ton of cash. The only prebuilt computer I would ever consider would be an Apple, but that has yet to have happened.
While Vista may be a POS in some peoples eye's I have had no problems with it. Other than the fact Creative labs has totally failed to deliver a 100% bulletproof driver for my OS, but that is not MS's fault.