Horizontal, because when spinning a disk in a vertical position, you have:
F(side moving downward) = F(motor) + F(gravity)
F(side moving upward) = F(motor) - F(gravity)
Now, F(Gravity) is the same for both sides, and F(Motor) must be the same due to the fact that they are being spun by the same motor.
This means that the difference of the forces != 0, which means there are mismatched forces while spinning which can lead to damaged disks. Now, I assume Nintendo has accounted for this, but even so - better safe than sorry.
EDIT: I realize that the difference in forces is minute, and my math is very simplified; I just prefer to play it safe, and don't wanna type out the actual math. I have done it in a more thorough fashion though 
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fksumot tag: "Sheik had to become a man to be useful. Or less useful. Might depend if you're bi."
--Predictions--
1) WiiFit will outsell the pokemans.
Current Status: 2009.01.10 70k till PKMN Yellow (Passed: Emerald, Crystal, FR/LG)
