I think you mean the per-user settings. They are in /home/user/.<name of application>. To delete settings of a certain app, for example one called 'some-app' do the following:

- Open xterm. By default you are in /home/user/
- To see all folders and files in there type: - Suppose you see the folder ".some-app" in the results. Remove it and its contents with or back it up with The application files themselves (not the per-user settings) should normally be removed automatically if you install and uninstall using the application manager. Only if you install using .deb files copies of packages remain. In that case you need to use apt-get clean and apt-get autoclean to get rid of them, or use apt-get remove --purge <name of app to be uninstalled> to uninstall the app and delete the package copies.