carrots. lots of carrots.
I haven't gotten to house my test pedals yet, but I'd say side to side, buttons on top, and DC input front. You don't want to step on the DC cord and rip it out, so it being away from you is good. You dont want the audio cables to hang in their sockets from the top, creating a danger where you can hang your foot up in them if you get too close, and so on.
These would be my design preferences.
Spacehog's "In the meantime." Is one of the best rock bassists ever.