Ever single fan controller I've ever owned has annoyed me. Now days new motherboards come with half decent fan control now days so it's not such an issue and that's a lot of the reason this project (originally started on an Arduino) has not moved on.
Basic design:
6 analog inputs to measure temperature of various components around the computer.
6 Fan controls, some PWM, some basic on/off.
Self contained so if the PC locks up the fan control still works.
USB interface to the PC so settings can be tweaked and measurements made.