As a 772 driver I still find it unbelievable that we have the ability to turn off the transponder in flight. I was firmly of the opinion that this option would be removed post 9/11 after it became apparent how difficult it is for ATC to track aircraft without a working transponder.
I can think of no reason you would EVER want to turn off the transponder once in flight, and I think that we will find this option is rapidly removed from the flight deck..