Joshua, my thought is that, other factors being held constant, there is no significant functional difference. If a sub driver is suitable for firing downward(i.e. it can withstand the "sag" involved in that positioning)and if the enclosure size, port tuning, etc. are the same, then it should be essentially identical regardless of orientation. The fact that the center of the driver is a few inches closer to the floor when firing down shouldn't lead to it being "boomier"; as long as it's within about 1/8th wavelength(say 20 inches)of the floor and both walls the bass will be adequately supported in either orientation.
I did a quick Google search to find something worthwhile on this and think sonicdesign.se/subplace.html covers it pretty well, despite a somewhat awkward translation from the Swedish.
