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.
GEDXchange is a collection of genealogy tools to work with GEDCOM 5.5 and GSF 2.0 files. These tools allow you to create and edit GEDCOM 5.5 Genealogical data files, create Web pages from GEDCOM 5.5 files, export data to GEDML, view contents of genealogical data in various ways, convert GSF 2.0 data format to GEDCOM 5.5, and validate GEDCOM 5.5 files.
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.
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.
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.