AppTrap detects when apps are trashed and asks if the user would like to trash prefs as well. Very nice solution, way better than AppZapper.

http://onnati.net/apptrap/

Don't see whey we can't write a project that solves this problem on a general level with a similar method. When a .app appears in specified folders ask to move it to an applications folder. Watched folders default to ~/Desktop and ~/Downloads and the app folder defaults to /Applications.