JDiff is maybe also worth a mentioning.
  JDiff is a Javadoc doclet which
  generates an HTML report of all the
  packages, classes, constructors,
  methods, and fields which have been
  removed, added or changed in any way,
  including their documentation, when
  two APIs are compared. This is very
  useful for describing exactly what has
  changed between two releases of a
  product. Only the API (Application
  Programming Interface) of each version
  is compared. It does not compare what
  the source code does when executed.
As I understood it runs on the sourcefolder of the old version and generates an xml file. The same for the sourcefolder with the new version. Than the two xml-outputs are compared and a changelist compiled. In html-javadoc-api-style