Last year we mounted our RC vertically, it worked fine...though the rest buttons were at the bottom and kind of a pain to get to. Plus it was hard to wire some of the stuff towards the bottom - though that may have been since it was very close to other componets.
Everything else should be fine...cept I think verticle speed controllers would just suck up more metal scraps.
This year the one thing our programmers wanted (well one of the things) was having the RC mounted flat so that it was easier to get to (though we're extended all of our wires from it - the reset, the prog switches and the tether and program ports).
We were thinking of putting the circuit panel vertically, but it seemed kinda hard to push the breakers in and we were afraid it would have enough support.
Overall it doesn't matter, just make sure things that need to be visible (i.e. the RC) are and things are easy to get to if need be.