This trick might actually work with more cards than just my Nvidia Geforce 6600 GT card manufactured by MSI. The default fan noise is so irritating that I was looking for ways to either turn it down by software, bios upgrades or replacing the fan. I preferred the software method over flashing the bios over buying a new fan that could replace the old one. After consulting google with search terms like geforce 6600 fan speed, reduce fan speed geforce and similar strings I finally found a forum entry that was about the problem I faced.
A guy suggested to use the freeware RivaTuner which he said was able to reduce the fan speed of my video card by altering the fan speed directly. This was the solution I was looking for. I quickly downloaded and installed Rivatuner. The only thing left was to lower the fan speed and make the changes permanent.
I clicked on customize in the first screen that appeared right next to Forceware detected and selected the icon for system settings from the panel. The second tab was named fan, the goal of my search. I was able to define a fan speed value for three different states: standard 2D, low power 3D and performance 3D. I changed the settings from 100% to 25 in standard 2D mode, 50% for low power 3D and 100% for performance 3D. 2D means everything that you do normally in windows like using office, surfing the internet or writing an email.
I checked the box that saved the settings and applied them at every system start and voila - the noise was gone. From one second to the next it was gone. My pc is almost silent now, the noisiest part is my external hard drive, everything else is almost silently. (I bought a low noise cpu fan and power supply).
I suggest you take a look at Rivatuner if you face a similar problem like I did. It might solve yours too