Layout on high-end gaming computer. please comment.

Go with the 64 bit vista, get 8gb or ram, stay with the gtx 280 and as I love DFI and because of current RMA problems with ASUS, I say get a DFI motherboard.
This is my next board.
http://www.newegg.com/Product/Prod [...] 6813136053

The most important component for gaming is the VGA card. Get the best one that you feel comfortable buying. The GTX280 is a fine choice, and will be able to play anything out there very well. It should cost about $400. Some go higher because they are factory overclocked to the tune of about 10%. That premium does not seem worth it to me. Others are more expensive because they have factory installed water cooling. Also not worth it to me.
The 4870X2 is the new card on the block. In general, it is more capable than the GTX280, but it comes at a premium price of about $550. Is it worth it to you?
Remember, that these cutting edge cards will be somewhat dated in a year.

At the level of the E8500 or Q9650, the vga card is much more important for gaming than the cpu.
Today, very few games can make use of more than two cores.
Flight simulator X is an exception. It is not a trivial matter to code multi threaded programs,
and game vendors will not sell too many games that require quads to run.
I don't see this changing in the next couple of years.

Net: E8500 or E8600 for the increased clock speed.

There is no need for a premium priced motherboard unless you are planning on dual vga cards. You should be able to get a Nice P35 or P45 motherboard from Asus or Gigabyte for <$100.

I happen to like fast hard drives, and the raptor is good. The velociraptor is even better, and it DOES make a difference. I like the strategy of a fast small system drive and a slower large drive for storage and backups.

For ram, get 4gb in a 2x2gb matched kit. It preserves your option to upgrade to 8gb. Unless you are multitasking, there is little value in 8gb. Most games and applications are written in 32bit mode.
DDR2-800 from a quality vendor is fine. Faster is not much worth it. Think 1-2% inframe rates vs. synthetic benchmarks.

Vista home premium-64 is good. Do you qualify for an academic license?

---good luck---

^ +1 to geofelt

If you don't mind waiting, Nehalem + HD 4870 X2, forget about nvidia.