The WAS6 server is a J2EE server. There is a 'feature pack' you can install that will allow you to deploy EJB3.0 components, but I haven't seen it used too often.
IRAD 7.5 is out in beta, and it comes with a WebSphere 7.0
test environment, both of which support EJB3.0 components.
I've actually been blogging about my experience with Rational Application Developer 7.5 and WebSphere Application Server 7.0. Feel free to check out some of my observations:
WebSphere 7 and IRAD 7.5 Tutorials and Blogs -Cameron McKenzie