The only downside to mounting a hd upside down would be that the circuit board of the hd would be exposed more than normal to the wires running accross it and touching it. I know that older harddrives like back a while ago had restriction on how the hardrive could be mounted, but most modern day drives has no restrictions at all. Considering most severs run hardrives on there sides I dont see why you would have an issue, but if anything read the documentation that comes with the hd and see if it does have any restrictions.
Phenom 9850 x4, Asus MVP Deluxe , 8gigs OCZ ddr2 1066, Visiontek 3870x2, Xfi Elite,2x WD Raptors 10k in raid 0,Antec 1000watt, and Cooler-master Stacker 830 Evolution.