If components on your HD controller boards are your big concern... flip the drives over and let the heat rise off of them.
My two 120Gig 7200RPM Maxtor drives only get hot when I don't have a fan on them (quiet, squirril cage design). I am thinking of a water block to put between them... but, after looking at the various designs here, I think I will just make a block that can sit on the base of the motor of each one and have the drive flipped upside down so that the motor and controller board is on top.
/me runs off to do some design work...
