Tom's Hardware: Topic Placement of fans in case to stop overheat
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It's generally best to have your intake fans at the lower front of a tower case; they draw in cool air from a low altitude. The exhaust fans should usually be placed in the upper rear of the case, where they draw out warm air (basic law of physics: warm air rises above cooler air). It's also common to have an intake fan in the side panel, blowing right onto the face of the motherboard, and sometimes an exhaust fan in the top of the case.
Generally it's better to have more intake pressure than exhaust pressure in your case, and to have filters on the intake fans. This creates a positive-pressure system where air only comes <i>into</i> the case through the filters. Having the reverse effect (a vacuum inside the case) causes air and dust to be sucked in through unfiltered holes, leaving dust bunnies all over your components. 
Kelledin
[dave@discovery ~] kill -9 1
init: Just what do you think you're doing, Dave?
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