I'm not sure, really. If it's at top, I'd ensure that it's not running at too high revs and interfering with the airflow past your processor and vid card. Perhaps rear/adjacent to the processor would be the best position, if it fits there!
I don't like 120mm fans personally, I think they're too big.
My own 'beast' has this setup:
Front/bottom - 92mm intake
Rear/centre - 80mm exhast
Rear/top- 80 mm exhaust
Power unit - 80mm intake, 80mm exhaust
Front/top- 2 banks of 3x40mm intake, to cool hard drives
It's a server case, and the fan positioning ensures airflow past the processor and vid card in the bottom section, and past the hard drives in the top section.