Open Source / Non-Proprietary
Hierarchy is an application and API to graphs Java class inheritance relationships.
Hierarchy can display tens of thousands of classes in a single graph, and scan through thousands of Java archives in seconds. It generates high-resolution, book-quality images, and is easily extensible.
More than that, Hierarchy provides a relatively simple example of how to use the rich Prefuse API (for graphs) as well as the BCEL API (for class file analysis).