For allmost all pumps orientation is not an issue. However I have expirimended with some Iwaki pumps (wich are awesome in every way) and some of them have bearings and magnetic shafts that shift with their orientaint, causing them to rub in certain positions. But most pumps used by watercoolers: Eheim, ViaAqua, Hydor, MaxiJet, etc, generaly wont have any issues being mounted upside down or sideways.
Best of luck to ya,
-Iron Hawk