Mine's vertical...smaller footprint, more surface area exposed for better heat dissipation...and, sadly, because I think it looks better. Haven't had or heard of anyone else have a problem w/ scratched discs.
Either way, don't stack stuff next to or on top of it. Had I placed it horizontally...knowing me, I would have already stacked up all sorts of stuff on top of it. So keeping it vertical keeps me (and others in the house) from doing that.