I use Sun
Java System Application Server 8.2 to prepare for my SCBCD. I know it's meant for J2EE 1.4, but it's still quite similar to the one for J2EE 1.3. You still need to do a little bit of tweaking if you plan to use Sun Java System Application Server 8.2, though.
Sun Java System Application Server isn't a standalone EJB container, but a full-fledge J2EE server. You can also try the reference implementation for J2EE 1.3.