Of the two types of pin connectors it's usually a tradeoff. The 4-pin can handle more potential difference without problems, but the 3-pin usually has that nice RPM monitoring built in, with typically three 3-pin fan headers accessible on the motherboard. Stick with the 3-pin connector if you have the option.
There are 2 pin fans too, basically just 12V and GND, without the RPM monitoring. Basically that's what the "4 pin fans" with Molex connectors are. Only 2 of the pins are actually used, the 12V and the GND.
if it's a big fan, with high cfm, and uses a 3 pin, u might wanna think about getting a 3 pin to 4 pin converter, people have burned out motherboard from putting huge fans on 3 pin and drawing too much voltage
Or you could just cut up the stock connector and connect it yourself to a standard 4-pin Molex connector, disregarding the fan monitoring lead. Its not rocket science, it takes just a minute.
I prefer 3-pin over 4-pin. I think my PS has crappy power regulation, giving too much juice to my 4-pin fans. But the P3V4X has giant power capacitors to combat that, so my 3-pins get the right amount of juice.
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