Currently an EJB / Web Application project uses a JBoss-specific JNDI configuration file, placed either in the conf directory or in the Jar file (both works fine).
How can I make this project portable between JBoss (4.2.3 or 5) and GlassFish 3? Is there a recommended way to set different JNDI configuration parameters depending on the container?
According to their EJB FAQ, Glassfish developers have put a jndi.properties file within appserv-rt.jar. The JNDI machinery in Java SE automatically detects this file when used in conjunction with no-arg InitialContext() and bootstraps the correct naming provider.
My understanding is that this should work in Glassfish also. Did you try do deploy your application without the jndi.properties file specific to JBoss (and to place it into the conf directory when deploying on JBoss)?