It's all in the motherboard. Everything else is an easy upgrade as you feel it's needed. Even the motherboard isn't that bad. I haven't bought a new 'system' in years, but over time everything has been upgraded a few times. Just make sure you initially buy something you can upgrade. Keep in mind that a lot of Dell, Compaq, etc systems are proprietary and hard (impossible sometimes) to upgrade. Not that they aren't great machines. Dell has some really nice deals and configurations but in my experience once they have your money their service is horrible. I've heard great things about HP customer service but have no personal experience there.
Some companies geared towards high performance gaming machines are:
http://www.outsideloop.com (VERY nice guys and always willing to help)
http://www.hypersonic-pc.com (where my system originally came from...the seem a little pricey these days though)
and the place I order most of my stuff from:
http://www.zipzoomfly.com (formerly googlegear)
I don't know anything about their systems as I've only ordered parts from them, but they have good prices.
There's always pricewatch, but be very careful there. Scammers are everywhere. Make sure you verify that the company you are ordering from actually exists.
http://www.pricewatch.com
If you wade through the mud there are some good deals to be had.