JGenea is an pure Java genealogy application useful to store information about the members of a family, the relationship between them, acts (birth, mariage, death, etc.), and photos. JGenea can import gedcom files from another applications and export all or part of your data to gedcom files, PDF files, patronymes/towns files, and backups.
GenealogyJ is a full-featured standalone Java application that can handle all of your genealogic information. It provides different graphical components for working on your family tree and is GEDCOM compliant. It requires a Java 1.4 Virtual Machine and runs on Windows / Mac / Linux.
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.