GML4J is a Java API for facilitating work with the Geography Markup Language (http://www.gmlcentral.com). GML is an XML-based framework for encoding geography information adopted as a recommendation paper by OGC (http://www.opengis.org).
CityBuilder is an attempt to automate much of the work involved in creating large virtual urban landscapes. The system takes a street map as input, and produces street geometry and a scene graph as output. Applications include games (think GTA*), etc.
GeoClass for PHP provides classes to handle georeferenced data. It can search databases which contain latitude/longitude for a location to find locations within a surrounding area. Conversion between data formats and distance-calculations are provided.
Geoblock is a program for 3D modeling, database management and visualization of geoscience datasets. It is designed for mineral deposit exploration, ore reserve estimation, mine planning and simulation of processes in mine sites.
GeoTools is an open source java toolkit for developing interactive geographical maps. The emphasis is on client side mapping applets which require little or no server side support. The main file format for the moment is the ESRI shapefile