GooTool uses the Java Preferences system to store your settings and preferences. Thus it depends what platform you're using:

Under Windows, the settings are in the registry under: HKEY_CURRENT_USER\Software\JavaSoft\Prefs\com\goofans\gootool

Under Mac OS X, the settings are in the user's library, e.g.: /Users/david/Library/Preferences/com.goofans.gootool.plist

Under Linux, the settings are in the user's home directory, e.g.: /home/david/.java/.userPrefs/com/goofans/gootool/