This week's book giveaway is in the OO, Patterns, UML and Refactoring forum. We're giving away four copies of Refactoring for Software Design Smells: Managing Technical Debt and have Girish Suryanarayana, Ganesh Samarthyam & Tushar Sharma on-line! See this thread for details.
You can usually get by with just using the ejb-jar.xml if you do not want to do anything vendor-specific with your EJBs (or whatever resource you are describing with your DD.) I ran an entire enterprise application using JNDI look ups for the data source and the ejb-jar.xml to define BMPs. The minute you want to migrate to CMP or something that requires tie-in with the container, it will be time to use the jboss.xml or whatever container specific file fits your app server.