Jon Udell: Patterns of persistence takes a bold stance on separating persistence in J2EE from relational databases. I agree with his points and I now have to go play with JBoss 4.0 to see what they have cooked up. For anyone interested in a simple but powerful object database (similar to ObjectStore but no post processing) I would recommend Db4o. I have not used it in any production applications but I am looking at using for my blog visualization tool.
Several years ago Sun had a project to put orthogonal persistence into Java - I am not sure what happened to it but seeing what can be done with Db4o I wish they had continued.
However for most enterprises the technique for getting persistence into the application is not the major issue it is the integrity of the backup and restore solution. This may be getting easier with RAID drives but it is still an issue that is key to any robust persistence solution.
PS Jon, when are you going to enable comments on your blog?