I've only had my Makerbot Replicator for less than a week, and I was already tired of the level of fan noise when the machine is idle. My job requires me to be on the phone when I work from home, and people could hear the fan blasting over the phone. So, I tracked down a larger, lower RPM fan to replace the tiny, angry little fan in the Replicator.
I tried doing a solid mount with a metal bracket, but too much fan vibration was being transferred to the case. The noise was only moderately better. I then tried suspending the fan between 3 zip ties, and that isolated a majority of the noise. You can watch this vid to see a comparison of the original, the direct mount, and the zip tie mount:
Doing this means that you can't have the bottom cover in place. However, fan airflow is greatly increased with this 80mm fan, so the board should run even cooler.
The installation of the fan meant that the fan would touch the table surface if the normal rubber legs are installed. I removed the rubber legs on the base and replaced them with Bench Dogs, which are normally used in woodworking as anti-slip mats. The double-neoprene coating isolates a lot of the Replicator's movement during printing, making the unit quieter overall. They also add about an inch to the unit's height, allowing ample clearance for the fan.
As a side note, the small fan appears to be the same one used on the extruders. So, you'll end up with a spare fan as a bonus.