They don't have to sit directly on the bottom though. If you plan on having a base, either comprised of case feet or something that will raise the bottom of the case off the off the desk, then 1 to 2 inches should be fine.
Of course, with "desk clutter" being the variable, only you can decide what suits you.

(General Septem)
Ooh, there's an idea 
Optical drives on the bottom layer though? I would think it'd be better to have them up at least a few inches so that desk clutter doesn't interfere with the drive bays, is there a particular reason why you prefer the HDDs above the opticals?

Optical drives on the bottom layer though? I would think it'd be better to have them up at least a few inches so that desk clutter doesn't interfere with the drive bays, is there a particular reason why you prefer the HDDs above the opticals?

































