I can tell you that you will get better price/performance by custom building, but at the cost of no tech support and only manuf. warranty on parts. Especially since you already have your own OS, you can get a lot of extra value.
I'd personally suggest getting an AMD CPU between the $90-115 mark. You won't need more than 500W, so there are some great PSUs under $50... I don't have a great memory, so I can't remember which ones... lol.
For AMD, you'll be looking at AM3 socket, either Athlon II or Phenom II... the Phenom line is better for gaming, but costs a bit more. This means that when you pick out your mobo, make sure it is AM3 socket and check that it supports DDR3 memory as it is cheaper than DDR2.
I build this for about $400 shipped & taxes:
Cheap family computer ideas?
This might be a good starting point... Still, you have a bigger budget, so getting an upgraded CPU and GPU will be the first priority.
AMD phenom II x4 955 BE - price match to $127
Buy Gigabyte [GA-M68MT-S2P] Gigabyte GA-M68MT-S2P mATX AM3 GF7025 NF630A DDR3 2PCI-E1 1PCI SATA2 RAID Video Sound Motherboard - $50
could get the same PSU, but I'd suggest finding a better one @ 450-500w - $50
4GB DDR3, most brands will do - $40 (kingston value ram works well)
Optical drive multi dvd/cd +/-r/rw burner - $16-$20 (any will do)
HDD & case & OS = you own already
= That puts us at about $310 with tax.
I'm not sure if you have to buy nVidia graphics to go with the nvidia chipset on the mobo... but I think you do.
I would look at getting a GTX 460 1GB, you can get them new with mail-in-rebate for under $170 with tax or you can get a used one. Getting a used one for under $150 shipped is worth looking into, since it won't be older than 6 months.
If you want to spend any leftover cash, look to buy a after-market CPU cooler or upgrade your mobo or GPU. You can also see if there are any combo deals or any price matching you can do to get better prices.