[Saintly]

I would say that sucking the air in the front and pushing it out the back is the way to go as the PSU also pushes out the back.
seperating your hard disks so air can circulate between them (if possible) is a good idea. a few fans infront of them or a disk drive cooling bracket will help a lot.
What CPU cooler do you have? the thermal paste will help with the contact between the cpu and the heat sink but is limited by the ability of the heat sink.
Useing round cables (floopy and DVD drives) and SATA cables for the drives (i assume you have SATA drives, if not use round cables) will help a lot with air flow. also try to secure the cables out of the way to help.
what model case did you put this all in??