Controlling a USB power supply (on/off) with Linux

Note. The information in this answer is relevant for the older kernels (up to 2.6.32). See tlwhitec's answer for the information on the newer kernels.

# disable external wake-up; do this only once
echo disabled > /sys/bus/usb/devices/usb1/power/wakeup 

echo on > /sys/bus/usb/devices/usb1/power/level       # turn on
echo suspend > /sys/bus/usb/devices/usb1/power/level  # turn off

(You may need to change usb1 to usb n)

Source: Documentation/usb/power-management.txt.gz

According to the docs, there were several changes to the USB power management from kernels 2.6.32, which seem to settle in 2.6.38. Now you'll need to wait for the device to become idle, which is governed by the particular device driver. The driver needs to support it, otherwise the device will never reach this state. Unluckily, now the user has no chance to force this. However, if you're lucky and your device can become idle, then to turn this off you need to:

echo "0" > "/sys/bus/usb/devices/usbX/power/autosuspend"
echo "auto" > "/sys/bus/usb/devices/usbX/power/level"

or, for kernels around 2.6.38 and above:

echo "0" > "/sys/bus/usb/devices/usbX/power/autosuspend_delay_ms"
echo "auto" > "/sys/bus/usb/devices/usbX/power/control"

This literally means, go suspend at the moment the device becomes idle.

So unless your fan is something "intelligent" that can be seen as a device and controlled by a driver, you probably won't have much luck on current kernels.