I find alon944's post confusing. His "fix" may be based on the less-common color coding used on some AMD CPU fans with Black, Red, Yellow and Blue wires. For the more common system of Black, Yellow, Green and Blue, see again this link:
http://www.allpinouts.org/index.php/Motherboard_%28CPU%29_4_Pin_Fan
Now, if you are trying to connect to one of these 4-pin connectors on the wires from a fan, you need to know the color coding of the standard 4-pin Molex connector (comes from the PSU) used to provide power to older IDE devices, etc. See this link:
https://secure.wikimedia.org/wikipedia/en/wiki/Molex#Molex_connector
So, if you're trying to connect a 4-pin fan to some other power source connector, realize that the FAN's connector has Ground on Pin #1 (BLACK wire) and +12VDC on Pin #2 (normally Yellow). NOTE that this is NOT the same as the Yellow wire on a 3-pin fan's Pin #3, which is the speed pulse line. On a 4-pin fan's connector, the speed pulse line is still on Pin #3, BUT its color is normally Green.
To get a 3-pin OR a 4-pin fan to run, you need to provide Ground to connector Pin #1 and +12 VDC to Pin #2. Then it will always run at full speed. If you want it to run a slower speed, you still supply the +VDC signal to Pin #2, but it should be reduced to a lower voltage. That is what all speed controllers for 3-pin fans do, whether they are separate third-party devices or mobo pinouts. You do NOT need to connect anything to Pin #3. It takes the speed pulse signal (2 pulses per motor revolution) generated by the motor back TO the mobo so it can be monitored and display the motor speed. This signal is NOT necessary for the mobo to accomplish fan speed control - that is done based on actual temperature measurement separately, and accomplished by changing the fan +VDC voltage. However, mobo's do monitor that fan speed signal to be sure the fan is still turning.
A 4-pin fan NORMALLY receives +12 VDC on Pin #2 at all times, PLUS the special PWM signal on Pin #4 (normally a Blue wire). Within the fan there is a tiny controller chip that uses the PWM signal to control actual flow of current from the +12 VDC supply to the motor. The design is backwards compatible with 3-pin fan designs in two ways. First, the connector will fit on, connecting the first 3 pins to exactly the same signals in each case. Secondly, if the 4-pin fan receives NO PWM signal on Pin #4, it passes all the power available from Pin #2 to the motor. Now the power coming out of a 3-pin pinout on a mobo has the voltage on Pin #2 vary according to desired fan speed - it is NOT always +12 VDC. So a 4-pin fan plugged into a 3-pin mobo pinout WILL function and will change its speed.
Now, what about trying to connect a 3-pin OR a 4-pin fan to a separate fan speed controller. The controller output connector only has TWO lines - Ground and +VDC (varying from 0 to 12). It has NO PWM signal for Pin #4, and many controllers have no use for the speed pulse signal coming back from the fan on Pin #3. So to make this work you should be connecting controller Ground to fan Pin #1 (Black), and controller +VDC to fan Pin #2 (normally Yellow, but sometimes Red). Do not twist any other fan wires to anything else - leave them unconnected. Now, IF your fan controller actually does have a way to use the fan's pulse speed signal on Pin #3, then you should connect that one, too.
One small problem with these systems is the start-up situation. A +12 VDC fan motor needs a certain minimum voltage to start up - probably about 6 to 9 volts just briefly. When a mobo is doing the controlling, it is always set to provide full 12 VDC at start-up, and then drop it down a few seconds later as the actual measured temperature becomes available. BUT if you are using a less sophisticated fan controller unit pre-set to some low voltage, it may no be enough to start the fan. At start-up time you should briefly turn up each fan's speed (voltage) control to full, then reduce it to the desired setting.
What about feeding power to a fan directly from a 4-pin Molex power output from the PSU? Well, look back at that drawing of it. The Molex has +12 VDC on Pin #1 with the YELLOW wire, and Ground on Pins 2 and 3 (Black wires). Pin #4 with the RED wire does NOT have 12 volts - it has +5 VDC. So you must connect fan Pin #1 (Black Ground) to either of the Black wires of the Molex, and fan Pin #2 (Yellow or sometimes Red on 4-pin fans, and always Red on 3-pin fans) to the YELLOW wire of the Molex. NOTE that, if you connect a fan's Pin#2 by mistake to the Molex's RED wire, you are giving it only +5 VDC and it may not start up!