RefDB is a reference database and bibliography tool for SGML, XML, and LaTeX documents; provides most of the functionality of Reference Manager or EndNote.
Pybliographer is openly developed for managing bibliographic databases; supports several bibliography formats (BibTeX, Refer, Medline, ISI, Ovid) and can be used for searching, editing, reformatting, etc.
UPPAAL is an openly developed project for modeling, validation, and verification of real-time systems; includes controllers and communication protocols.
G3D is a C++ library for game developers, researchers, and students; not a stand-alone graphics or game engine, but a set of pieces to jump start your own engine or graphics project.
Impact is an openly developed program for simulation of dynamic events such as car crashes or other large deformation events; kept very simple to make it intuitive to use and easy to change and extend.
Xrefactory provides code completion, source browsing, and refactoring functions for Emacs and XEmacs; based on full pre-processing, parsing, and static analysis.
XDrawChem is an open source program for drawing chemical structures; features include fixed length and fixed angle drawing, a ring tool to automatically draw rings, and more.
The Basic E-Learning Tool Set (BELTS) provides a basic set of tools for using and managing learning objects; server allows for multiple schools to be hosted on the same system.