Use motherboard PWM to control non-PWM fans with MOSFET
There is a well established standard for the 4 pin PWM fan output on Motherboards.

The PWM output is open collector BJT or FET so needs to be pulled up externally to 3-5 V.
The PWM frequency should be from 21-28 kHz and from 20% to 100%. 
The reason the PWM does not go below 20% is that many fans will not start or run at the lower speeds. The computer BIOS will normally start the fans at 100% for several seconds on power on to get them started, then backoff to temperature controlled speeds. Some BIOS's will allow you to set a minimum fan speed higher than 20% or to set 0% to turn the fan off completely. 

The fan PWM controller is also responsible for counting the Tach signal, this is used to detect slow or stalled fans. If you don't enable this (supply the Tach signal to the controller) you might find your fan controller continually raising the speed of the fans. The solution is of course to feed the signal from one fan back to the motherboard controller.   

I'd suggest a low side fan drive like this would work:







simulate this circuit &ndash; Schematic created using CircuitLab

The FQP30N06 you mentioned in the comments would work but if you look at Figure 1 in the datasheet you have to remember you are operating on the extreme left hand side of the graph where V(DS) approaches zero. You will see here that to ensure good operation you really need to have a V(GS) of abut 4.5 V to assure a current of 2 A and a V(DS) of 0.1 V. 



There are a stunning new class of low V(GS) threshold FET's like the IRF7401 that feature Gate thresholds in the 1 V range. These can operate directly from 3 V microprocessor ports, but unfortunately they typically come in small surface mount packages ...so not particularly hobbyist friendly to wire up.