Here is a collection of useful posts on Derby or JavaDB from Sun. The first article give a good overview of how to write an application using JavaDB in desktop applications. Of course, there is support for JavaDB in NetBeans 5.0 including application container clients. Finally, Cheng describes different ways to manage JavaDB and has some tips in case you are trying to run Derby scripts from the command line.
The Java DB Community Page
has other useful links and bloggers, including