An artificial life simulator project that can also function as a genetic programming system. Written in Java with a graphical interface. http://www.generalnegentropics.com/archis/
An artificial world of lifeforms which eat, move and reproduce. Each species is controlled by a program, and you can write your own lifeforms. http://www.geocities.com/peterstephenbailey/
Floys are flocking Alife creatures having a territorial awareness: they defend their territory against any stranger. Floys are implemented in Java applets with free source code. http://arieldolan.com/ofiles/JavaFloys.html
An aquarium simulation written in Java. The program uses neural networks for all of the fish being simulated, and the fish are artificially evolved from random starting information. http://sourceforge.net/projects/jfish/
BugBots is a game, sort of. Really it's a project in Artificial Intelligence, and Object Oriented Design with heavy abstraction. http://bugbots.sourceforge.net/