I sided with the "BUILD YOUR OWN" side. There's plenty of info online if you need a few pointers (or as 20something adults say,

ing google it!). A quick search offered this link:
http://digg.com/tech_news/How_to_build_a_sweet_gaming_PC_for_538
(keep in mind that the article is from June 2007, so make sure when you are sourcing components that you are looking at newer parts)
If you don't have a Fry's Electronics store within a reasonable distance of your home, try the following websites just as others have suggested:
http://www.frys.com/
http://www.newegg.com/
http://www.tigerdirect.com/
You'll save yourself a ton of money this way. I just built my first computer, a HTPC rig. From start to finish (installed O/S, programs and updates), it took me about 4 1/2 hours. As a newbie to building a PC, the only true drawback is the inevitable headaches that come from learning on the fly -- easily remedied by aspirins and/or booze (if you're old enough).
One last thing: the O/S. More than likely, you'll be using Vista Premium or Vista Ultimate. I would suggest that you find a reputable retailer, online or B&M, that sells an OEM version of the O/S (NewEgg does, BTW). Nothing sucks more these days than having a "new" copy of the O/S, only to find that it has been registered previously or you have a bootleg. Keep in mind, an individual purchasing an OEM version still gets updates and genuine validation but IS NOT eligible for Microsoft Tech Support if needed. My past experience with MS tech support has been so-so at best, so I feel that I'm not missing anything by not paying the additional $20-$80 for a retail version. Plus, you might get lucky and find a good deal. For my HTPC, I'm using Vista Ultimate 64-Bit OEM which I purchased at a local Fry's on sale for $169 -- and it came with a $50 gift card that I received before I left the store! Hell, at least 75% of the components I purchased came with a rebate on top of its sale price!
Using a free, open source O/S like Unbuntu might work, but it would test the nerves of the inexperienced, requiring a world of patience, and might not work at all for what you need your PC to do. My gut tells me that someone out there with a bunch more experience than I have has made it work, so you never know.
Good Luck.
EDIT: OOPS, I forgot motherboards. I'm using a Gigabyte board (GA-MA78GM-S2H) which I can't really complain about (except their tech support is unable to answer heavily specific questions). My uncle builds custom PC's as a retirement hobby and depending on application and CPU, has used Abit, Asus, and MSI. Word on the street says avoid ECS -- QC isn't up to snuff.