A Prefpane style app, automatically asks if you want to move associated preference files when you move applications to the trash.
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Pro Prefpane style app
AppTrap installs a daemon that runs in the background monitoring the trash, when you drag an app to the trash it will search for associated .plist files that have been left behind and ask to move them to the trash. In other words, AppTrap launches and does the work for you automatically. All you have to do is uninstall apps the old fashioned mac way by dragging apps to the trash.
Con Requires using Finder
Does not work if you trash app using alternate file browser like Path Finder.
Con Gets some things, not everything
This is thorough enough in cleaning up most of the cruft that gets left behind by applications, but might not get everything for the more invasive applications, especially if some of the files have privileged permissions.