There are a couple of differences. Low output pickups drive the front end of your amp less and tend to produce a more bluesy or more vintage distortion. They have a very open feel to their tone. High output pickups drive your amp harder and can sound more compressed with a tighter feel. Also, higher output pickups with the same magnet type tend to sound darker because the resonant frequency of a larger coil is lower than that of a smaller coil. Medium output pickups tend to fall somewhere in between depending on their magnet and wire type.
WRITTEN ON JUNE 15, 2015, BY