ok Speedfan is the standard freeware for controlling fans, give it a go. For some mobos it really doesnt work though, I cant use it on my gigabyte.
best thing to use is mobo software, what is the model of your mobo i'll find a link for you.
one final thing, you can only change the fan speeds of fans with small 3 or 4 pin connectors to the motherboard. any fans with large molex co0nnectors that are plugged straight into the PSU will run at 100% speed all the time.