If you look at the motherboard, only the CPU fan header has a MOSFET
next to it. That MOSFET controls the voltage setting to the CPU fan.
The other headers have no control (and if you use an ohmmeter, you'll
find the +12V pin on the other headers, is connected directly to the
+12V wire on the 20 pin ATX power connectors).
Products with the "Qfan2" feature on this page, have more than one
fan control channel. You have to download the manual and make sure
how many channels each one has, as you cannot trust Asus that way.
http://usa.asus.com/products/mb/feature.htm
There are a whole bunch of drive tray fan controllers made,
but as far as I know, only one or two of those products actually
contain smart fan controllers. One product has a profile for
each fan type (CPU fan is turned up at a different temperature, than
the chassis fan). You will have to search pretty hard to find
that product (I don't have a URL handy).
http://www17.tomshardware.com/howto/20040615/fan-controller-06.html
These have a fixed profile, and no differentiation between the needs
of a chassis fan and a CPU fan:
http://www.silverstonetek.com/products-fp52.htm
http://www.atechfabrication.com/products/fan_speed_controller.htm
This one interfaces via USB and allows the main CPU to control
the fans - it is called the "T-balancer":
http://www.tomshardware.com/howto/20041122/index.html
Paul