80MM fans are smaller and must move faster to move the same amount of air that a 120MM fan can move and slower RPMs. 120MM fans tend to be quieter and move more air. A 120MM fan is a bit smaller than twice the size of the 80MM fan but it moves a whole lot more air. Get 120MM fans if you can...
Difference is mainly in noise. The same fans in 120mm format can push more air with the same rotation speed or push the same air as a 80mm fan would do, but at a lower rotation speed. Lower speed = lower noise.
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