Norman Richards describes How JEE was Saved.
Norman (a JBoss guy, BTW) contends that Hibernate and Spring helped bring needed improvements to JEE (see Java SE 6 and Java EE 5). Now that EJB 3.0 is pretty much final, and incorporates the best parts of Hibernate and Spring, Norman contends that their necessity has passed and their importance will wane. (For some history, see Persisting Domain Objects and Unnamed Persistence Specification.)
I agree with him that standards are good, that having these features built into EJB and JEE will provide a consistent foundation for using these features.
Norman also points out an interesting purpose that these alternative/extension frameworks may serve: Not so much a basis for long term (many years) software development, but a temporary fix that shows how the standards can and should be improved. Once the standards are improved thusly, the frameworks are no longer needed and should go away. For example, Struts was the basis for JSF; once you have JSF, do you still need Struts? Probably not.
Ultimately, I still contend that IBM clients who have spent money on products like WebSphere Application Server and Rational Application Developer are better off sticking with the related J(2)EE programming model as much as possible, so as to maximize their use of standards and of IBM support.