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.
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.
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.
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.
Hissim is a history generator for WorldForge project. It uses simulation to create communities of creatures with realistic relationships and backgrounds. It's distributed with a threaded Tk interface and a simple globe viewer. Hissim can generate GEDCOM so you can edit its output with genealogy programs.