the 3 pin varies its speed by changing the amount of power sent to the electromagnets in the fan changing how hard they pull

the 4 pin varies its speed by changing WHEN the magnets fire. that blue wire controls when the magnets are activated, the yellow is the RPM sensor, red is pos, and black is neg

the 4 pin is called PWM or Pulse Width Modulated, and is alot better at controlling the speed