Airflow is an important factor in thermal management. The consesus is:
Intake on the front
Exhaust on the rear
Intake on the side cover (if applicable)
All unoccupied openings should be covered or filtered.
I think that your PCI slots on the back ought to be covered. If you do not have an exhaust fan on the rear you could mount an 80mm (or largest/quietest) in the PCI openings w/ zip-ties. Though not ideally at the top of the case, it will help.
There is the "control-freak" notion of negative/positive air pressure. Though nominal in pressure it can make a small (1-2C) difference. To avoid this use fan controllers to balance the airflow.
Okay, I'll shut up now....
Oh yeah, here are some case mod links:
Check out the blowhole and fan grill mods for cooling.