Sometimes things go a bit wrong. Sometimes they go very wrong. XKill is a simple little application that allows you to kill a running X application that has got out of kilter. Think of this as a quick way to get back control of your Desktop.
On desktop setups where icons are shown on the desktop these are normally taken from the specific folder ~/Desktop. If you find you want to show icons from either your Home or another directory for a particular install/user you can do so by editing the user-dirs config file as described here.
Debug Gnome Shell, or run it from the console, either for plugin development or troubleshooting.