[Zogthetroll]

using the 5 1/4" bays would be the easiest solution, you can go a couple of ways with that, either go the cheap route and get the U-shaped drive bay adaptors, or spend more and get an enclosure that will cut down on noise & vibration, maybe even watercool(a bit extreme though). The other thing you could do, depending on whether you get a full tower or not, is to mount the 3 1/2" bays above the power supply, in front of the rear exhaust fan, like the old-school server style cases.