Originally posted by: furballi
The key variable is the INTAKE air temperature to the CPU cooler. When pulling air from the MB side, the intake air going to the CPU cooler will be HOTTER due to the heat from the surface mount devices on the board. Of course these devices on the board will run cooler, but the cooling capability of the CPU will suffer due to the higher air intake temperature. The efficiency of the cooling fan will also degrade due to the higher air flow resistance on the intake side.
If the case vents well, then the CPU cooling fan should always blow into the case for best cooling performance.