Fan speeds are generally controlled by Voltage (3 pin fans) or PWM 4 pin fans. A 4 pin MoBo header for a fan is no indicator that it is PWM or variable voltage. CPU Fan headers on a MoBo are PWM but all the other 4 pin headers on a MoBo (well 99.8% of them) are all DC voltage control despite whatever the advertising says.
Case fans are most commonly 3 pin and controlled by voltage....so if you run it off a 12v feed, that fan will spin at 1500 rpm ....run it at 7 volts it will go slower .... run it at 5 volts, it will go even slower. You can hook it up to any one of those voltages via a molex connector picking the correct colored wires for each voltage and a ground.
Yellow and black = 12 volts
Black and red = 5 volts
yellow and red = 7 volts
More here
http://www.techpowerup.com/articles/other/137
You can also use a rheostat for control via knob, use a fan controller or just plug it into one of the many fan headers on ya MoBo.
PWM works similarly but it always sends 12volts..... if voltage control is compared to a bicycle where to go faster you pedal faster (apply more voltage) .... PWM is more like a skateboard where ya push off w/ ya foot always with the same pressure (12v) but to go faster you just increase how often ya push.
BIOS control is generally limited. Many MoBos come with utilities like Asus FanXpert2 which allow you to create fan curves base dupon CPU temp.... a generic one that works on may MoBos is SpeedFan.
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