Orientation of asymmetrical brake pads on front vs. rear
Some of the KoolStop pads have a ramp at the leading edge (facing in the direction that the wheel rotation comes from – i.e., towards the back of the bike) that is supposed to help sweep water and other contaminants off of the rim. If you have these you'd want to face them in the right direction if you can.

Other than that and clearance I can't think of a reason why it would matter unless the pads are the type with replaceable cartridges in which case you need to make sure that the open end of carrier faces towards the rear so that the pads are pushed forward against the stop.