Part of the EJB 3 spec is a sub-spec known as the Java Persistence Architecture or JPA. There's been talk of actually breaking JPA out of the EJB3 JSR, since it virtually erases the high-level differences between EJB, JDO and Hibernate.
No, JDO doesn't go extinct QUITE yet. BEA (formerly Solarmetric) Kodo V4 supports JPA. In fact, a group of BEA Kodo employees are at the core of the Jakarta OpenJPA project.
Similarly, Hibernate 3 is now actively supporting JPA. In fact, I used the OpenJPA reverse mapping tool to create Hibernate mappings and have been prototyping a webapp using Spring's new JPA support to handle the grunt work.
Once I've got the app fully functional, I'll probably switch it from Tomcat+Hibernate to JBoss+EJB3 just to say I could.
I'm going to be a "small government" candidate. I'll be the government. Just me. No one else.