Well, I'll tell you since I have been working with these boards for a bit now... its really not bad.. I have an Intel Core2Duo E6400 system (Desktop CPU, intel DG945FC mobo if I remember the model correctly) inside an original NES case with a thermaltake meOrb HSF unit. It runs like a dream and the NES case has NO Externally visible vent additions with the exception of the rear exhaust fan (60mm). It is in a small, enclosed cabinet in my tv stand and I have had no heating issues. My next project is to put one of these into a mbox m350 mitx enclosure that mounts on the back of a monitor (VESA 75 standard if I remember correctly, maybe 100 though). You definitely don't need a huge case, you can actually go quite small on the form factor and pack a lot inside small areas, just make sure that your ventilation is adequate, it really doesn't take much to keep the systems cool. Now, if you want a hardcore gaming rig, these aren't what you want (Although the NES does do Half Life2 @ 1920x1080 with all settings jacked), but for a business setup, this is the perfect form factor. People just need to take the time to start making small cases for these boards (Well, companies are now, but not many are trying to make it really small) and start targetting the market that would benefit from these systems (Point of sale, etc.. and yes I know that they already are in these markets and have been for a bit, but broader adoption would be a good thing).
For some pics of the NES setup: http://smg.photobucket.com/albums/v145/ayrus/NES%20PC/