If you just want to be able to slow the fan down, a simple rheostat type fan controller can be installed in an empty 3.5" bay for about ten bucks.
If you want the system to control fan speed based on temperature, and if your motherboard does not support this, look at some of the more upscale fan controllers. Models range from about $15 all the way up to $45 at Newegg.com, for instance:http://www.newegg.com/Product/ProductList.aspx?Submit=ENE&N=40000011&Description=FAN+CONTROLLER&Tpk=fan%20controller
If you're looking for something more exotic, check Xoxide.com:http://www.xoxide.com/5fanco1.html
I run a lot of older Duron and T-Bird based machines still, and a lot of overheating problems with them were traced to the heat transfer medium in use at the time. Sometimes just lifting the heatsink will reveal that heat transfer paste has migrated away from a hot spot. Cleaning the sink's mating surface and refreshing the paste or tape and then re-assembling is sometimes enough to bring the temperature down such that the system will automatically slow down the fan.
If all else fails, buy a larger, slower fan and a transition shroud. This will enable your system to move a larger volume of air but more quietly.
There are also acoustic dampening kits for fan mounts. (I've had good luck with automotive type low acid RTV for fan mounts, too. DON'T use the regular stuff - the acetic acid in it will damage your computer as it gases out during cure.)
Good luck with this one. Quieting down a noisy enclosure can be a challenge, but this problem seems pretty straightforward.