The motherboard
For our motherboard chipset, we'll be going with the Intel 965. This decision locks us out from running a full-speed ATI Crossfire, but the P965’s new memory controller should be an interesting proposition. While 975X platforms continue to offer excellent performance, the 965 runs a close race. The other reason I’m going with P965 is that my plan is to go micro-ATX on this machine...

What?!
And now, we're introducing our gimmick for this system building article: our stated goal for this system build is to create a micro ATX system that outperforms last year's Dual Opteron Ultimate Workstation for workstation applications, outperforms last year’s Ultimate HTPC for media applications, outperforms last year’s Ultimate Desktop, and even outperforms our original Budget Storage Server… all in a micro-ATX form factor.
[Ed: And now the story begins…]
Our micro-ATX motherboard of choice for the Core 2 Duo will be the Gigabyte GA-965GM-S2. Gigabyte’s standard ATX P965 Express motherboards have been the favored platform for Core 2 Duo enthusiasts. The ATX motherboards offer excellent overclocking performance as well as stability. In the case of the micro-ATX system, we’re giving up solid state capacitors for high-quality Nichicon capacitors and giving up a few PCI and PCI-e slots. The GA-965GM-S2 also features an ALC883 which should be perfect for our S/PDIF only HTPC design.
Historically, micro ATX platforms have been shunned by enthusiasts. If you wanted upgradeability, you'd go with a standard ATX motherboard. If you wanted portability, you'd go with the even smaller SFF.
Gigabyte GA-965GM-S2
$125
Running Total: $475