Sound wise, it really won't make a difference. *You have to worry about ventilation though. *Usually... the power supply goes on the top, then fx units, preamps, and
power amps in the bottom (some people have seperate racks just for power amps.) *It is sometimes recommended that you leave an open space above or below some of the peices that cause lots of heat. *Also consider weight of each unit, heaviest towards the bottom.