Building a PC
What’s the difference between SYS_FAN and PUMP_FAN sockets?
Pump fans normally run at 100% all the time. Sys fans are either constant or can be set to scale with overall system temperature.
4 pin fan headers work through pulse width modulation (PWM) whereby the controller is alternating very quickly between 0% voltage and 100% voltage (I think it’s 12 volt max, but I’m not sure so I’m using percentages) to give the illusion of a voltage between the two. It changes the duration of the pulses (hence pulse width) in order to tend more towards full or zero voltage. I.e. 1 part zero and three parts full voltage would come across as 75% voltage.
3 pin fan headers actually change the voltage itself between zero and full voltage (9 volts for 75%).
The reason 4 pin is generally considered better is that the fan motors are spec’d to work at a single voltage (12 volt) and so supplying with a smaller voltage via a 3 pin doesn’t have them operating the best they can. Additionally, most motors have a minimum voltage just to start spinning (edit, think static friction because that’s basically what it is), so you lose a lot of the low end fan speeds. With a 4 pin header, the fan can just get a short burst of full voltage to spin at low speeds within spec of the motor.