Using EAR or WAR depends on the server you want to deploy it, your application, and on your personal preferences. From Java EE6 you can package your EJBs together with other servlets, jsps etc into WAR file (you end up with web application which you can deploy only on java ee 6 compatible server). If you package your app the old way with ejbs in a separate package and war separately, you can use java ee 5 server if you haven't used other features of java ee6 within your application, you can separate the deployments of your EJBs and WARs to have a clear separation of your business layer (EJB) and your view (Servlets, JSP's etc).