It depens, there are 2 kinds of heatpipes. Those with wicks, which work in any orientation and the cheaper wickless which rely on gravity. It really varies with Motherboard Manufacturer. Abit's newer boards have wicks, as do EVGA. Asus are the awkward ones as they won't say. However my mobo mount is ATX inverted & i've run a commando & p5k Deluxe without issue.
The the convential Vertical mount is the normal orierntation the wickless pipes are expected to work.
luck
