I haven't noticed this before when I upgraded an OS or changed iPhones - but perhaps someone else can confirm.. I haven't emptied my trash (on a mac) since I upgraded to the iPhone 4. I just went to empty it and saw a bunch of apps (.ipa) in there. Now I checked and they all still seem to also be in the correct iTunes directory as well - so ultimately not worries. But just wondered how/why some (not all) apps wound up in the trash.