Our new portal app is entirely running on EJB3 beans and we have no problems what so ever.
We use Spring portlet to wire up UI, my Spring deployer to inject fine grained beans into EJB3 components and Hibernate EntityManager implementation for persistance.
Any word on when JBoss Seam and Facelets will work in the Portal? That will make EJB3 really cool for portlets.
What the does EJB(3,2,1) or any of that have to do with a Portal Server and or portlets? Well-designed portlets should ideally be only concerned with processing events (clicks, etc.) from the UI and/or rendering content in the correct view state AND dispatching an event to an appropriate business object (be it an EJB, a POJO, or whatever). Looking up an EJB, a POJO, or whatever shouldn't be an issue at all....
In many cases, simple portlets will use the portlet-preferences system of a JSR168 portal server for persistence of custom-user preferences.