I recently printed out Jeff Atwood's Understanding The Hardware blog post and plan on taking it to Fry's Electronics and saying to them "Give me all the parts on these sheets so I can put this together." However, I'm going to be installing 64bit Windows Server 2008 on this machine so before I get all the parts:
Will all this hardware be 64bit Server 2008 compatible? - i.e. all drivers available for this hardware for this OS?
Yes, all that stuff should be fine (motherboard and CPU hardware, motherboard drivers, video card drivers).
You have a $1000 operating system license and you're going to put it on ~$1100 worth of hardware purchased at Fry's and presumably put together by yourself?
Hardware's generally pretty OS-agnostic (at least in terms of Windows flavors) these days. Your only concern is getting drivers for other devices (scanners, printers, IR remotes) that won't work on 64bit and/or won't work on "Server" OSes. Online backup software like Mozy generally won't even install on a Server OS, so it depends on what you're going to use it for.
That said, if you're just going to use it for a home machine, then without even looking at the hardware list Jeff put together, I'd be confident in saying it'll probably work just fine.