You can configure your standalone Java app to read configurable properties from a properties file (say conf.properties) on the server.
You may have a UI webpage (html/jsp) with all the field to be configured. When the page is submitted a JSP/Servlet may write/update the contents of conf.properties on the server.
UPDATE: The above solution will work assuming only an admin user wants to update the properties file.
In case anybody should be able to update it, then concurrency issue has to be taken into account.
In that scenario, you have to implement a mechanism similar to how weblogic10 updates config.xml using Admin Console.
i.e. You will have 2 conf.properties files confA & confB (initially in sync). The standalone app will always read from confB. The UI will have 2 buttons say Lock & Release configurations. When an edit is made (locked & released), it will be written to confA and at the same time changes of confA has to be replicated to confB.