Short of the plug computers and comparable devices, you're looking at Pico-ITX for the smallest, readily available form factor that still resembles a typical PC.
The Via Artigo 1100 (and soon to be released 1150) are:
5.7" x 3.9" x 2.0"
You'll pay way too much for the degree of performance. The first (1000A;
http://www.silentpcreview.com/via-artigo) was based on the C7 (1GHz, single core) and reviews complained about noise levels and performance.
The next (current) revision (A1100) swapped the C7 out for a Nano 1.2GHz single core. Reviews complained about heat, since it seems Via ramped the fan down at the cost of making the system toasty. It remains to be seen if the dual-core A1150 improves performance and reduces heat output enough to be tolerable. The current sheet does not inspire confidence with respect to power/heat output (similar power draw specs vs. A1100), so we'll have to see about performance.
http://www.e-itx.com/artigo-a1150.html
The first-gen C7 version was actually threaded for mounting into a 5.25 bay. Later revisions seem to be a bit smaller overall (but possibly 0.2" taller at 2.0" vs. 1.8"), but I don't see threading for 5.25 bay mounting. I'm sure a little creativity would still allow you to have a PC-within-a-PC.
There are fanless Pico-ITX Atom systems as well, but they are even pricier.