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#11
For best cooling in general for air cooled computers with internal case heat sinks, you want the most amount of air moving through the computer. This means a well balanced intake and exhaust setup with a good general airflow direction. Generally I prefer top and rear exhaust and front and side intake.
If your case is more than cool enough, then you can have a reduced airflow to help prevent excess dust moving through and settling in the case.
In my case, most of my fans are 4-pin PWM fans which are speed controlled on custom curves I've setup based on CPU temps. My video card exhaust fans are speed controlled based on the GPU temps. My top 200mm exhaust fan isn't though, and it just has a resistance based three position switch. I usually have it set to "low" or "medium." Currently it's set to medium.
My computer is OCed and dynamically fully loaded and crunching for scientific research on the CPU and GPUs nearly 24/7.