All you need to do is manually stop the various fans one at a time and determine which one is the loudest. Focus on quieting that one, then move on to the next loudest sound, and so on. In the pc world, companies like Zalman make a little resistor box with a knob that you can put in-line with the fans to reduce their speed manually. Not sure if these would be compatible with the Mac, or if they would interfere with the software fan control, but this is how we used to do things before software control became common.
Saying that - it seems like somebody must have written a little program for OSX to give you control of the fan speed?
DONT do the first bit and yes people have written fan control software.
I developed Fan Control from the MacBook Pro fan control software of someone else. Personally I think dynamic fan control is better than SMC Fan Control...
My Mac Pro is 2 feet away from my face, and I cannot hear anything coming from it. There is more sound from the default fan speed from my Macbook Pro than my Mac Pro.
I doubt that somehow, mines 2 feet away from my face with all the fan speeds turned down and I can *still* hear it.
Not that it bothers me.
Main sources of noise:
4870 fan (GT120 is silent in comparison) and the Hard-disks.