Not much more I can add to FullMetal's remarks, except that some motherboards don't enable the PWM control capability on all of the mobo fan headers.  So they only report fan speed and power the fans, but you cannot control pulse-width-modulation and fan speed.
The newer mobos from this last year probably allow control of more fan headers.  My current board is 2004 vintage, and I can only control the CPU fan-header with Almico's SpeedFan.
The front-panel controllers can be a plus with some people -- I have one, but I'm not always fiddling with it.  Since all my fans work in series within an air-ducting system, then intake and exhaust fans are set at a constant speed, and the CPU fan speed rises and falls at a temperature threshold.  There is enough of a seal in my duct that the exhaust fan speed doesn't matter much -- the CPU fan just pushes more air through those ports at the higher temps.
My view is that these things can best be performed through motherboard headers with programs like SpeedFan, and if the control feature is not enabled, some sort of USB-connected fan-control card can be feasible or desireable.  For instance, the Sunbeam "Theta" controller allows for software control of all fans connected to it.  It is made to fit in a PCI slot, but this is just a convenience of the manufacturer's making.  They've chosen to use a spare PCI slot just to hold the card, but there are no gold edge-connectors -- the card doesn't get power from or communicate with the system through the PCI.   Therefore, it can be mounted elsewhere in the case -- leaving that slot free for something that would need to use it.
Like so many other makers of USB devices and hubs, Sunbeam created their card to connect externally to a USB port -- thus the PCI approach to securing the card.  But if it is mounted elsewhere in the case, you could simply run a shielded USB wire to the motherboard USB plugs.  
I guess they're trying to make it easy for noobs, dummies, and the electromechanically challenged.