Haven't myself but I've heard (and seen) of it being done. Most important things are that it has enough ventilation to cool the machine and that you can get access to any components (or remove and install new ones). Also if it's going to be water-cooled and your building into it it's own coolant storage tank like my buddy did, build the tank and any connections for the system below or segregated from the electronics area incase of a leak or maintenance (if it wasn't for that little thing called gravity, he would of built a perfect hand-made case his first try, but instead he goofed and KIAed his motherboard the first time he tried to drain and refill the coolant tank, lol).
