If you had $2000

I'd probably do something like this. I've never had an Intel desktop before, so if I had the money, I might as well. No case, keyboard, or mouse though. I'd reuse what I have because they work. As for an OS, I would use one of the keys I obtained from the MSDNAA.

However, if I were to apply the $2000 towards my existing machine, I'd do the following:
64MB cache, 2TB, WD Caviar Black HDD x 2
Blu-ray Burner x 2
Silenx 120mm Ixtrema Case Fan x 3
Replacement 140mm top case fan that could support silicone fan mounts
Package of silicone fan mounts
Some SSD for a primary drive
Retail copy of Windows 7 Professional (perhaps Ultimate if I was so inclined to blow money away)
AMD Phenom II X4 965 Black Edition
ATX mobo with 2 full x16 PCI-E slots and DDR3 1333+ support
ATI 5850 (5870 is too big for my Antec 300)
Black media reader to place into the 3rd 5.25" drive bay.

If adventurous, I'd try for sound elimination (perhaps sound insulation or liquid cooling, though I'm not sure how quiet the latter could be).

EDIT:

Actually, I'd probably hold on to my current mobo and use the money saved to reassemble my previous pc and set it up as a NAS or media server.