After having installed OS X Tiger one year ago when I got the beast, I found the mess in /Applications annoying, so I created sub-directories and moved stuff around :

• Internet (Safari, Firefox, Adium, etc)
• Multimedia (VLC, iMovie, iPhoto, etc)
• Office (Neooffice, Addressbook, iCal, etc)
• Tools (the goodies I add)
• Utilities (all the small Apple stuff)

and so on.

During OS X “Software Update”, I had already noticed that applications always came back to /Applications, not to their subdirectories. Eg iTunes update created /Applications/iTunes instead of /Applications/Multimedia/iTunes. A drag-and-drop fixed it.

However, after upgrading to Leopard (using Archive and Install, I’m not that optimistic), all the Leopard applications went back to /Applications, ignoring my stuff under the subdirs. It took a while but using PathFinder, I could identify the old versions and delete them. Being a little bit optimistic anyway, I re-moved all the Apple stuff in their subdir. I hope Apple will do a better job the next time.