On RivaTuner under "Driver Settings" (second half of the first page) click "customize" and then "system settings". From here you can change your graphic cards clocks etc, but up at the top there should be a little tab called "fan". Click that and you've got control over your fan.
Depends what graphics card you have and what drivers you're using though.
That's all I have to do to change the speed on my two GTX260s, but on my old 8600GTS cards the cooler was plugged into the motherboard headers and had to be controlled with an ASUS program.