yWorks has released a new version of yDoc.
yDoc 2.1 is a javadoc extension that lets you:

* Exclude classes, fields, and methods only by adding a exclusion tag (y.exclude),
but allows for sophisticated custom filter criteria also.
* Define custom tags via an XML based mechanism
* Automatically generate and incorporate UML diagrams in your API. The look
of these diagrams is highly customizable.
yDoc currently generates these diagrams as SVG, compressed SVG, JPG, ...

In version 2.1 the following features have been added:

* Automatic generation of UML package structure and package dependency diagrams
* All UML diagrams now feature hyperlinks, which allow direct access to the
documentation of the displayed packages, types,
and type members.
* Refined customization capabilites for all types of UML diagrams
- exclusion of types by name in UML relations
- multiple heuristics to define dependencies
- elimination of transitive dependencies in package dependency diagrams
* An easy-to-use GUI-based style editor

yDoc 2.1 is available at:
http://www.yworks.com/products/ydoc/