Hmm, well most fan controllers (the nice quality ones) have 3 pin fan connectors on them. However , on my work pc I have a very crappy fan controller I got on ebay that does use molex connectors and not 3 pin fan connectors.
I did just find this tho , should work fine. Comes with little connectors so you can use either 3 pin or molex.
http://cgi.ebay.com/Fan-speed-Contro...QQcmdZViewItem