In general front and sides are intakes and top and back are exhausts, this keeps the air flowing from the bottom front up to the top back. Having the side be an intake gives a nice injection of cool air right onto the CPU or GPU which usually does more good than sucking some hot air out.
Feel free to experiment with the fan setup in your case and see what setup works best.
Filters are usually only put on intake fans, but you can use them on your exhausts too, it will keep dust from slowly working in while the system is off. Rather than buying a real air filter you can make one out of lady's nylons if you are feeling crafty.
Personally I've got a couple old cases that at this point I'm clueless the name/make any more, but my side fans are best used as intake. If I set them to exhaust they actually fight with the cpu fans for air and my cpu temps go up.
Side fans are placed to add cool air (from outside going in) to GPUs. The TOP fans and Back fans are designed to vent hot air out.
High end GPUs(2 PCIE Slot design) are configured to force hot air out at the back. This is a consistent reference design for both NVIDIA and ATI. This type of card design require more cool air. It runs cooler with side fans blowing in cool air.
I have yet to see a PC case that specify side fans to be configured as exhaust.
The side fans should be blowing air into the computer, if you configure them to suck air out of the computer it will still help with the cooling of the computer but not as much as blowing air into the computer. I asked myself this question sometime ago when I took off the side fan and couldn’t remember which way around it originally was, I then experimented with it blowing in both directions and determined that it was better blowing in to the case.