How would I go about controlling the output power of a USB port through software, I want to be able to control a 1 speed USB powered personnal fan.

Don't really follow your question but here is a link that might help:

http://www.usbman.com/index.htm

http://www.usbman.com/USB%202%20News.htm

USB speeds are 1.1 or 2.0

What is the make & model of this fan?

What sort of control does it require?

It is personnal fan (it cools me down) but can sometimes be a little loud, I want to lower the voltage being given to the fan, so I need to control the voltage output of a single usb port

Check the motherboard manual. It may or may not have such settings in the BIOS.