Speedfan can be used sometimes to alter fan speeds. Last I knew it still supported Windows 95 and newer. Here is the link to info about it. As seen in the screenshot at the wiki, you can set fan speeds by percentage so if you want to quiet a system down you can set it to like 70% etc, although be very careful with this as for you could slow a fan down to the point that it no longer cools the CPU/GPU enough and you can cook the system.
http://en.wikipedia.org/wiki/SpeedFanSupport for Speedfan to associate with older hardware is hit and miss depending on the system. Sometimes it will allow you to sense and make adjustments and other times it can not correctly initialize the hardware controls or the system is lacking a specific hardware control feature that otherwise would work with a different or newer system.
Speedfan is a good tool for looking at temps, but it can also be used to control the PWM ( Pulse Width Modulation ) to the fan(s) and so you can slow the fan speed.
Some info about PWM in relation to speedfan and its PWM controls.
http://www.almico.com/sfarticle.php?id=1