If I was starting from scratch, I'd probably go to tigerdirect and get one of their socket 949 athlon 64 barebones combos. You can get a great deal there, under $400 for a case, mobo, cpu, power supply. Then start adding the finishing touches. 80 gig hard drive for $60 more, Nvidia GeForce 6600GT or 6800, 1 gig (2x512 meg sticks) pc 3200 or faster memory, and you're in business with a system that is going to be within 10-15% of the speed of the fastest out there.
If you have the extra bucks, get a GF 6800GT or one of the more expensive X800 vid cards. I have a GF6800GT and it's a nice match to my Athlon 64 3200.
If possible, get a 90nm "winchester" socket 939 athlon64 since they run cooler and maybe a bit faster than the older socket 939 cpus, but they'll probably cost just a bit more.