@bigfoot catnap: err, not necessarilly!
It all depends on your specific motherboard... You'd have to empty the case and test your mobo in there. A full-ATX mobo will most possibly have some problems. Check the other thread where i took my project http://eab.abime.net/showthread.php?t=50463
You'll notice that i placed the motherboard vertically to the rear. Which means that cards won't face the case slots. In my case i don't feel uncomfortable with this, because i intend to extend every card's jacks to metal plates like i did with the MacMini's extensions..
(slight soldering skills are required)