Depends on what you want this system to do.
I'll assume some of the most demanding tasks things like:
(a) 3d gaming
(b) 3d rendering
(c) audio/video editing, encoding, burning
(d) compiling
(e) database searching

Someone here mentioned a board with dual opteron 250's. Yes! I would start
there. I have some experience building high-end PC's (but not with a $6,000
budget! Wow.) so I'll give my two cents.

Dual Opteron 250's - makes for much better multitasking. Try having a single
FX-51 like I do and multitasking sucks.
Not sure what motherboard but I bet some other learned person on here will
recommend a great one.
Four 200 gig SATA drives mirrored and striped so you have performance AND
data safety. OR if you price this thing out and have lots of extra money,
get fastest SCSI instead of SATA.
If you go SATA route, depending on your motherboard, you may need to get a
RAID card.
FOUR gig of fastest dual channel RAM your motherboard supports.
BFG's 6800 Ultra OC - someone here said the XT800 is faster or something.
They are mostly wrong. The XT800 is not much more than a souped up ATi 9800;
The 6800 line is new technology and much more advanced. I won't go into
details but you can research this and find your truth. Most modern cards
will support two monitors simultaneously.
Lian Li case. Get whichever one you want. I just recommend this brand for
cases. Research and see why. They rock.
Antec True power supply. Get a biggy like over 500.
Get a name-brand DVD/CD burner like Sony or something. You usually can't go
wrong with Sony.

Scott
System built January 2004:
FX-51 on MSI K8T800 Master-2 FAR board
Nvidia 5950 Ultra 256meg
1 gig fast DDR ram (two 512MB sticks)
two 160gig SATA drives mirrored
Lian-LI PC70 case
Antec True 480
blah blah blah