I've got some limited experience building my own computers. I got an MSI motherboard, and it was a bit bare bones, features were locked, the PCI express slot only supports certain graphics cards, and I had to RMA it for a bad SATA controller, which took 24 days.
My roommate got an AMD BioStar, and it seems quite top of the line. The packaging and accessories were top-notch, and the bios has built in overclocking features, so his dual core 2.0 runs stable at 2.5GHz with just a couple easy setting changes. He also got a Radeon X1600Pro, and it runs Doom3 at just under Ultra settings quite well. You can get an X1600pro w/ dual link for $82 after rebate
here. If you want even better performance and you're not too worried about the cost, I'd go with the X1900. I don't know much about NVidia, though, and I'm sure they've got some great offerings.
Check around on eBay to see what cards like your current one are selling for to get a good price.