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.
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.
tngCalendar is a Web calendar addon to the TNG software for online genealogy. It adds a convenient view of your family history, overlaying anniversaries of births, deaths, and marriages on top of an easy-to-understand calendar. It can be dropped in-place over a commercial TNG installation, or installed in a parallel directory.
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.
MyNukeGenealogy is a plugin-module for PHPNuke or PostNuke to build up a family or surname Web site. It allows for displaying and editing genealogical data (individuals, families, events, notes, sources, etc.) and importing gedcom files (export functionalities will follow). It has a flexible template system to customise the layout and design.
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.