The ServerSide announced that Hibernate 3 is going beta. Looks good. The roadmap lists the steps forward to EJB3 support.
We’re using TopLink now. It would be interesting to test Hibernate in my next project to see how they measure up.
Oracle has an article on how TipLink intergrates with Spring Framework here.
I havn’t looked much under the hood of Eclipse, but it seems to me to be one of the most extensive and flexible open source products out there. I am really impressed by how it supports plugins, as well as their internal update manager. One example pf customization can be found here with creating a new splash screen as a plugin.