Really haven't noticed a change in fan speed in my MDD Dual 1.0 Ghz, to be honest.
Are you using the software program Temperature Monitor?
http://www.versiontracker.com/dyn/moreinfo/macosx/19994
It's a good way to track your CPU temps and correlate fan noise accordingly. For example, I find that when my CPU temps hit 60 C, the PSU fans speed up, so I'm locked in a constant struggle to keep temps below that. I've got the main 120 mm CPU fan running at a constant 7 volts, so it never speeds up or slows down.
I've got a copper heatsink sitting in the house, waiting to be put it. Have you notice that it keeps things cooler than the stock aluminum heatsink? I've got the Verax silencking kit over the CPUs right now, so I'm not sure if the copper heatsink will be able to keep things as cool as the VErax kit or not. (I hope so; would be nice to get rid of more fan noise, even though the Verax fans are VERy quiet.)
Finally, in addition to the Verax silencing kit, I just replaced (last night) my GeForce 4ti video card (has a fan) with a Radeon 9000 Pro, which is fanless. Still evaluating the performance tradeoff between the two (doesn't seem to be much so far), but I can already tell a discernible drop in fan noise without the GeForce fan in there humming away.
Good luck, and stay cool!
- bgordon