I tried several different fan configurations when I built my current machine. It's in an old Antec server case, 21H x 8W x 17D (inches) with several hard drives in it (too lazy to open it and count at the moment). It has the usual 5 inch power supply exhaust fan at top rear and four 3-inch case fans. Using on-chip sensors and an electronic thermometer to measure intake and exhaust temperatures, I took temperatures with various fan configurations.
Lowest operating and exhaust temperatures were with:
Front fan, intake blowing over hard drives (there is also a bit of open front area that seems to act as intake; dust build-up around there)
Side fan, intake blowing over video and other expansion cards
2 rear fans, exhaust from near the CPU
At one point I had a flaky memory stick and added a small fan blowing/circulating air between the chips.
FIlter material at the intakes is two layers of some open cell foam I had laying around. Other filter material, at least in the US, is available at the large-chain home improvment stores. Look in the heating/plumbing section for heating vent filters.
This is a floor-standing tower chassis and requires cleaning every 1 to 3 months depending on the local environment. Most cleaning is done with a damp paper towel to clean surfaces and wipe of the fan blades. The heatsinks, power supply, and unoccupied expansion connectors are cleaned with a squirt of canned air. The filters just need warm water and some squeezing.
I still run across the collected temperature data occassionally, but can never find it when needed, like now!
Cheers,
Tom