Hey mikey, it generally just comes down to your choice of cooler. Some coolers only allow one orientation, others will support both.... At least that true of AMD boards, not 100% about Intels.....
The Cooler Master Hyper 212+ or 212 EVO for example will allow for both orientations on AMD rigs. a Xigmatek HDT-S1283 will only go on one way as it uses AMD's stock retention mechanism. Can only blow up, not ideal if you case doesn't have top fans.