A good fan controller is the mCubed T-Balancer bigNG, although it is a PITA mixing and matching software and drivers to get it to work in Windows 7 64bit.
The manual is also a POS. The manual for the analogue extension set, showed an earlier revision of the unit I was using, so working out what connected where became trial and error.
Once you get it working it is a dream and very controllable (through s/w) including having options for automated fan speed control, temperature monitoring, flow meters, automatic shutdown, etc (although you will need extension sets to accomplish the latter two).
http://www.t-balancer.com/english/produkt_tban_bigng.htm
It is expensive, although you do not lose a drive bay and you can mount it pretty much anywhere in your case (it can connect directly to the USB header on your MB).
If you are wanting something more budget orientated, then other posters have given you better options.
Edit: To give you an idea of cost, in the UK the T-balancer and Analogue Extension set cost me £100 (or ~$150). I wanted the monitoring capabilities for my water cooling set up. I also found it difficult to find suppliers selling it in the UK (it may be the same in the US).