Motherboard header:
|| o | GND (typically Black)
|| o | +12v (typically Red)
|| o | Fan Speed (typically Yellow)
| o | Fan PWM
The top three pins are the normal 3-pin motherboard header.
Usually +12v is yellow and +5v is red, but this doesn't seem to apply to fan cables.
Jokester, I have a Swiftech MCP350, and it has a single blue wire to connect to pin 3 on the motherboard. I presume your pump is similar?
Helmutcheese (what a name!), the extra pin is for PWM control of the fan speed. Basically, what this does is switch the power to the fan on and off very rapidly. If the fan speed needs to be higher, the fan is 'on' more than it is 'off', and vice versa for a slower fan speed. If I use a standard fan on this header it will only run at 12v, unless I use a program like Speedfan.