As far as the fan speed programs go (the new one most of us are using as of yesterday, anyway), no one really knows in depth how it works yet. I can tell you right now, however, that if I open the program, adjust my fan speeds, and EXIT the program, the fans stay at the speed I adjusted them to. This would indicate that something on the system board is being changed. So, we have yet to find a way to let the fans go back to their default settings if one decides to get rid of the program.
On another note, I have my fans (all of them) running one notch higher than the default (constantly on) and my PC temp dropped 10 DEGREES CELSIUS. I MEAN WOW! Granted, I put my lappy to sleep when I go to bed, so it may be better for me than others who leave their PC's on all the time.