As a habit on Windows I typically organized applications into folders on the Start menu based on categories, Engineering, Multimedia, Games, etc. When I moved to Mac I did the same to my Applications folder. I know this is not the same since on Windows I was only moving shortcuts, and on OS X I am moving the whole App. I have never had a problem with the applications themselves running, the one problem that occurs quite often is when I use Software Update to check for updates I will frequently end up with multiple copies of Quicktime, Mail, Safari, iTunes, etc ... at the top of my Applications folder, or it won't find updates for programs I know are installed since they have been moved (iPhoto). I know why it does this, but why can't they utilize Spotlight to keep track of where I move my apps so that when I update they can simply update the apps where I put them rather than put a completely new copy where I don't want it? Do others have this same problem or does everyone else simply leave their apps at the top level of Applications?