Well since it was asked, there are certainly CF to IDE adaptors out there and are fairly common for mini-itx setups. SATA however might be another matter, I haven't kept an eye open for them in a while.
I am looking at doing something similar with the remnants of my workstation when the MB crashed, I can pick up an ASUS rackmount Dual-940 combo for about $250, and I have most of the other components. Benn looking at putting together a Pd processing box for shows that I would access via SSH and X-Forwarding to program as needed. Mini-Itx was something I kept a close eye on for a while, and stil keep an eye on for this type of purpose, but not to close lately. Not a bad project though.
Seablade