From Nikon's website:
Sensor cleaning takes approximately 3 seconds to complete. During this time a high pitched noise may be heard. This nearly inaudible squeal is just slightly louder with the D300 than the D700, and this may be due to the different sensors used in these cameras. The D90 noise is slight as well, but is audible is you listen closely enough.
My D90 makes a very faint "sqeak" and slight vibration. I can hear and feel this only if I hold the camera body against my ear (or very near my ear in a quiet room).
I wouldn't be surprised to find that different camera bodies make different sounds, since those vibrations would be felt throughout the camera body and anything, say a memory card, could vibrate and contribute to the noise. There are thousands of parts in there that could be vibrating. At least you can hear yours, and know it's working