For several years now I've used the mCubed T-Balancer. No knobs, no switches just a usb cable and some not so bad software. It also has a configurable automatic mode independent of windows. Two possible draw backs:
1) It relies on its own temperature sensors and cannot read the cpu temperature directly.
2) It uses PWM to control fan speeds, depending on your fans they may growl as a result. That said there is an analogue control version available.
You may also want to check out the aquaero from Aqua Computer. It is more focused on water cooling and my lack true independent control but I've heard good things about it.
Personally I how have my main fans driven from my mb header though I may get back to optimising my own diy controller one day.