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If you connect the molex, the fan will run at full tilt.
If you connect the 3 pin to the motherboard, the fan will run at the MB directed sensor speed.
Which you prefer depends on noise of the fan, and how much cooling you really need for where it is sited. i.e. no pint in using the motherboard if the sensor isn't related to the position of the fan.
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Motherboards don't tend to have a lot of fan connectors onboard hence they give you the option. As Rob says you use one or the other.. BUT only though 4 pin are speed controlled as the 3 pin only report back speed to the bios.
Oh, OK. There are only actually 3 wires coming out of the fan, so I guess then the only advantage with the motherboard connector is that I can see how quick it's moving, but can't change the speed, unless I add some kind of speed controller in between.
Other than that, it's which socket is easiest to get to.