I've noticed that the noise ONLY happens on certain games.

Games included in my collection that I've noticed the noise with, but likely not limited to:

Orange Box
Guitar Hero II & III

I've been playing a lot of Beautiful Katamari this weekend, and it doesn't spin down / stop the disc noisily with that one.

Perhaps it has something to do with the way the game data is formatted on those games and the way the 360 reads them.