I made a sample WebApp in May 2012 that uses JDO 3.0 & DataNucleus 3.0 - take a look how clean it is:
https://github.com/TorbenVesterager/BadAssWebApp
Okay maybe it's a little bit too clean, because I use the POJOs both for the database and the JSON client, but it's fun :)
PS: Contains a few SuppressWarnings annotations (developed in IntelliJ 11)