When storing preferences for applications on Java, there is a built in Preferences API. If you need full control of preference storage or need to change it from applications external to Java or manually,
one of the options I discussed last year may be better (if you need an XML file in a specific location for example), but if you just need simple cross-platform preference storage, the built in option is ideal.
Usage Summary
import java.util.prefs.Preferences;
Preferences prefs = Preferences.userNodeForPackage( getClass() );
prefs.get("keyName", "default value");
prefs.put("keyName", "new value");
The JavaDoc for it is quite confusing, so try this
tutorial on java.util.prefs.Preferences instead.