I have a XFX 9600GT on Windows 7 64bits.
Prior to my current Windows 7 64bits, I've had Windows XP, then Windows 7 32bits: Rivatuner 2.24c, ntune 5.05 & SpeedFan 4.43 were working perfectly. I was able to set fan speed and overclock with no problems.
Since I installed Windows 7 64bits, none of these work at all. I didn't try MSI Afterburner but I'm now using eVGAprecision2.0.3 and it works the way it should! It has profiles so it does automagically set the clocks/fan for up to 4 graphic cards, being able to set them synchronous/asynchronous. Give it a try it won't bite. ^^
eVGAprecision2.0.3:
http://downloads.guru3d.com/eVGA-Precision-2.0.3-download-2611.html
EDIT: it is a bit less sophisticated than rivatuner, but it do wonders on the 64bit edition of Windows 7 with latest 275.33 WHQL nvidia driver.