any issues or best ways up/down?

with a mix of hope/shimano/hayes brakes and pikes/totems/vanilla forks?

I have two fork up slots and one fork down slot.

never had any problems with mine – all hope brakes, mix of fox and RS forks

ours hang down the wall, held by front wheel hooks.
no issues to date with magura julies, avid j7, bombers or F100's…

I hang all of mine from the front wheel and I've never had any issues with forks or brakes – Hope, Shimano & Hayes Pace, RockShox & Manitou

Fox forks are best hung front wheel high as this will drain the oil onto the foam rings and improve lubrication.

Generally, I hang the suspension bikes up front wheel high (nice to keep the seals oiled, but you can trap oil in the wrong part of the forks and it might need a couple of bounces to sort it out) and the rigids front wheel down (it's more compact to have them like sardines)

I've had problems with two pairs of Rebas with bikes hung vertically. There's a tiny oil leak from the top of the Floodgate dial, from the damping cart. I spoke to TF Tuned about this, and they said the rubber washer between the blue dial and the Floodgate dial is a bit crumby, and best not to hang them like that if they leaked. A PUSH upgrade puts in a more effective (and no doubt expensive) washer and stops this leakage over time. I've had one pair PUSHed (and it does make a difference) but not dared hang 'em up. Or rather, not been organised enough to sort out the shed in the new house yet.