It's about the air flow. Ideally, you want fans blowing air into the case from one end and fans exhausting the air from the other end and that this airflow would cross over the major components to be cooled. Whether this flow is from front to back, back to front, top to botom, side to front, or side to back depends more on the case design and layout. Another thought is, if the cpu cooler fans are blowing the air down onto the cpu (as they should be) then you do not want the side panel that is right over top of the heatsinks exhausting the air. If so, they will be trying to use the same air to push in opposite directions, they'll be fighting each other and your cpu will be the loser. If the rear fan is exhausting air, then you would want the side and or front fans to be blowing air into the case. Another consideration is the size of the fan and/or the CFM's of the fans. Ideally, you'd want the CFM rating of the fans blowing air into the case to be about the same as the CFM rating of the fan exhausting air out of the case. This is to equalize the air pressure and to ensure a constant flow of fresh, cool air through the case and to reduce dead spots or cause stagnant airflow.