This might help you Well, commons-configuration is, like many of apache project, an abstraction layer allowing one to seemlessly use preferences, an ldap store, properties files, and so on. So, your question could be rewritten as is : Will you need to change the format you use to store your preferences ? If no, java preferences are the way to go. Elsewhere, consider the portability of commons configuration.
Commons - Configuration CompositeConfiguration and Preferences