Apache Commons Configuration works great. It supports having the configuration stored in a wide range of formats on the backend including properties, XML, JNDI, and more. It is easy to use and to extend. To get the most flexibility out of it use a factory to get the configuration and just use the Configuration interface after that.
Two feature of Commons Configuration that differentiate it over a straight Properties file is that it support automatic conversion to common types (int, float, String arrays) and it supports property substitution:
server.host=myHost
server.url=http://${server.host}/somePath