Of course, but at the time, the MoBo in my old system couldn't turn the fans off completely. I do believe most of them can do that now?
Also, running a waterpump off of the MoBo isn't the best thing you can do, although controlling your pump doesn't yield much benefit
About 1 year ago, i started working with microcontrollers, as one of my first projects i desinged a basic 6 channel USB-fan- / waterpump- controller.
I recently did a complete rewrite of the host-application and decided to open-source this baby for any computer-enthusiasts out there.