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Many applications have preferences panels that allow the user to choose a preferred appearance or behavior. The user's choices go into the user defaults database in the user's home directory. Note that only the choices that vary from the factory defaults are saved in the user defaults database. If you go to ~/Library/Preferences, you can see your user defaults database. The files are in XML format; you can browse through them with a text editor.
The NSUserDefaults class allows your application to register the factory defaults, save the user's preferences, and read previously saved user preferences.