Front panel fan(s) should blow air into the case.
Rear panel fans(s) should blow air out of the case.
Side panel fan(s) should blow air in.
Side panel fan(s) are usually mounted low to blow air into the AGP/PCI-E/PCI cards to aid in their cooling.
Some side panel fan(s) are mounted high to blow air to the processors heatsink/fan. I don't particularly like these because I'd rather it blow air to the PCI area.
Hope this helps.