dc42:
That should be fine, I've controlled a PWM fan like that, I think it was an Arctic F12 pwm too. Bear in mind that the Intel PWM spec only guarantees that fans will run from 30% pwm to maximum.
Look at what the OP said:
could I use a transistor as a switch connected to pin 3 set up so when the PWM duty cycle goes high it connect the grounds of the fans and allows me to throttle them that way?
I don't think he's talking about a PWM (4 wire) fan, but simply switching the fan on and off with the Arduino PWM output and the transistor.