I was wondering... The HMC is a little big (at least I haven't room for it above my amplifier.)

But hFX has actually made a smaller version of their nice HTPC case. In Denmark you can buy premade (passive cooled) HTPCs with this case:
http://www.mm-vision.dk/default.asp?men ... =visionhtp

They are only a little cheaper than the Genesi HMC, but they are a lot more easy to find room for.
How would a barebone Pegasos II MB fit into one of these smaller cases, and how difficult would it be to cool the processor?

sorry... wrong forum. It should have been "PPC - users". Please move it.

It will fit, CPU-card wise with 90 mm height.
No idea about the passive cooling though.