I just wanted to throw in a little "Rah! Rah!" here.
On December 3rd, we went live with the first version of our software that uses Derby and Hibernate for persistent storage. We have learned quite a few things on this journey, some of which are reflected in the implementation of DatabaseManager that is posted on the Wiki.
Some of the more interesting lessons such as the mechanism we implemented to update the database of our live application and how we handle multiple user threads came afterwords. Unfortunately, I can't post that code (the version of DatabaseManager on the Wiki was developed independently) however, if anyone is interested, I might be talked into writing a short paper.
I would like to throw a big "thank you" to all of the Derby developers. Without this product this delivery would probably have been much more painful.
P.S. The application is a tool used by astronomers who are preparing their proposals for time on the Hubble Space Telescope.