In addition to the Morex and Travla/Casetronic
cases mentioned earlier, there's the new LGX MK150
. It's a short-depth 1.5U rackmount case, but there's no reason you need to mount the rack ears. Pricing is probably overkill for your application, but it might minimize the amount of customization you'll need to do, as it will accommodate a FlexATX PSU, has two PCI slots, and, most importantly, good ventilation in a relatively small form factor.
The front plates are removable as flat pieces, so it would be easy to Dremel/saw any additional holes (more cooling, CD tray, 3.5" bay) you might want.