I find side intake fans are generally more effective. You can always reverse the direction and see what difference it makes to your temperatures, though.
I cut a hole and put a fan on the side panel blowing in. My case temps and hard drive temps dropped 10-15°F. The bad part is that now I have to blow lots of dust out on a monthly basis, even with a foam filter on the fan.
Don't know if this helps any but every single piece of elevator equipment I come across, they use their side fans as intakes and top mounted fans as exhaust.