It's more a preferance thing then something that should be one way or the other. On one had if the PSU fan is moving in air from the bottom of the case the air is soley cooling the PSU, granted, if the system is on the ground (more specificaly a carpet) then it might be harder for the fan to move air, plus you'll be getting a fair amount of more dust then if the fan was inside the case (and not on the floor as well).
With the PSU fan inside the case it helps move some hot air away from the hardware inside the system, but remember that the air going into the PSU will always be warm/hot which some people may not like(though i don't beileve it makes a huge difference largely considering that hot air rises so most of the air will be escaping from the top of the case.)
I personally have my PSU fan facing upward simply because i don't want the fan pick up dust and other crap from the table. But really it makes no difference to me.