WOW, I would love to have 3k to spend on a computer alone.
Since your'e probably going to get a crapload of responses, I will just talk about sound and video (probably every ones' favorite categories).
I'm assuming that the arrival of Doom 3 has sparked this need for a new gaming PC. Doom 3 is going to be revolutionary in two fronts, video, and more importantly, sound.
As for the video card, ATI is the leader for older video cards and today's mediecore video cards (200 dollar price range). When it comes to your highest quality video cards, NVidia has now taken the cake. As shown in the latest benchmarks, NVidia has done better than ATI. It is painfully obvious that the Radeon X800 Pros 4 missing pipelines are subjecting it to a big performance penalty with DOOM 3. So I would strongly suggest the NVidia 6800 Ultra.
VERY useful article:
As for sound, Doom 3 has revolutionized the gaming industry by being the first company to utilize both EAX technology and Dolby Digital. This calls for a need for a 5.1 or a 7.1 24 bit sound card. Your price range leaves alot of room for the very best. So I would suggest Creative Labs Sound Blaster Audigy2 ZS Platinum Pro PCI Sound Card, Model "SB0360". Also, when playing these games, I suggest hooking it up to a 7.1 Denon Home Theatre System using a long digital coaxial cable (thats if you still have the money left).
Let us all know what you purchase.