GWintree is a GEDCOM-based genealogy program. It provides facilities to record, view, edit, and merge genealogy data, and to produce genealogy charts, family trees, and reports in a range of formats, including HTML. Charts can show all relatives, ancestors only, or descendants only. HTML charts allow you to click on a person in your HTML report to see where they are on the chart. Automatic matching and merging of genealogy data between files is supported.
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.
Urdabrunn is a genealogy three-tier multi-user application suitable for former "The Master Genealogist" (TMG) users. The database and core functions are implemented in PostgreSQL. Some prototype interfacing has been set up in PHP, but the goal is for the main interface to be in wxPython or Qt.
gedcom4j is a Java library for loading (parsing) and saving GEDCOM 5.5 or 5.5.1 files to/from a Java object hierarchy, which can be manipulated by your code as you see fit. Please note that gedcom4j is not an application. It is a library for parsing, manipulating, and writing GEDCOM data in your own programs.