JPA (from Java EE 5) is an excellent example of the (over)use of annotations. Java EE 6 will also introduce annotations in lot of new areas, such as RESTful webservices and new annotations for under each the good old Servlet API.
Here are several resources:
It is not only the configuration specifics which are to / can be taken over by annotations, but they can also be used to control the behaviour. You see this good back in the Java EE 6's JAX-RS examples.