Morcego is a 3D graph browser for viewing and navigating any graph-like structure. Examples of such structures include social networks, site maps, hierarchies, and genealogy trees. It currently only support simple graphs. It's already integrated into TikiWiki. Morcego is not meant to provide a solution for the end user, but to be embedded in a Web application by developers. It's a Java applet that communicates with an XML-RPC server to load the graph that is displayed.
The Deimos Project is a 3D space combat simulator and modular game library collection. It includes a 3D modeler designed with a programmer's needs in mind. It allows you to construct 3D models by writing Java source code. All you need to design a model is a computer, some graph paper, and a pencil. The modeler's internals function as a simple OpenGL scene graph API, without preventing the use of low-level OpenGL commands. For storing settings and other hierarchically-representable data, the project provides a Hierarchy library that stores data atomically using XML. It also features a timing library, a game object container system, and many other features.