While I certainly prefer over, I did want to point out a time when I prefer under that hasn't been listed.
When in a commercial restroom with the half-ply toilet paper which has jagged edges around each side to 'easily rip' the toilet paper (even though you have to treat it like a paper thin sheet of gold ready protect a satellite preparing to orbit to keep it from ripping while unrolling), under is far superior so that your job of getting more than half of a sheet of toilet paper is sufficient.
Also, I have on a couple of occasions found my toilet paper unraveled for unknown reasons. I still haven't quite figured it out, but the problem seems to be tied to the density of said toilet paper (ie fluffy soft toilet paper not at as high of risk).
Ultimately, it doesn't bother me so much that I'll change the paper orientation or even pay attention to the orientation when installing new toilet paper, but do prefer over.
On a final note, if you own a business and get toilet paper that is so cheap it rips by the pressure required to remove the said toilet paper, just remember this. Those are the places that I make sure i have enough toilet paper to make a paper mache basket ball before i commence wiping. There are 2 reasons, first reason is a protest for the retarded notion this will save any money, and the second is because the paper is so thin i can't trust it so must use only large quantities.