Phylogeny and Evolution
Various projects in evolution, molecular evolution and phylogenetic epidemiology being carried out by members in the Department of Zoology at the University of Oxford.
http://evolve.zoo.ox.ac.uk/

Altruist
Free PC software package for simulating evolution in structured populations. Includes models for group selection, group territoriality, Wright's shifting balance model of punctuated equilibria and speciation.
http://www.agner.org/evolution/

AJ's Black Smoker
A java-based simulation illustrating natural selection in action, with a dynamic environment affected by simulated biological activity. Requires Java 2 plug-in. Contextual help, explanatory material available.
http://www.well.com/~ajmilne/black_smoker/

evolution@home
Designed on the model of SETI@home, this project makes evolutionary data available for download to, and analysis on, personal computers. Splitting up the work among a variety of machines results in faster results generation.
http://www.evolutionary-research.net

DarwinBots
An artificial life software in some ways similar to C-Robots and other programming games. Every simulated creature is a virtual robot with complex input and outputs and each DNA is a program that acts on a memory cells array. Freeware.
http://digilander.libero.it/darwinbots/

GALife
Watch creatures based on a neural network learn to solve simple problems (eating the right foods, escaping traps) through random mutations and selection of the fittest. Highly configurable, with a modular structure.
http://digilander.libero.it/galife/

Evolutionary Systems and Artificial Life
This course presents an overview of the field of Evolutionary Systems and its applied branch of Artificial Life. The historical and philosophical foundations of evolutionary thought are explored with particular emphasis on computational simulations of its models. Topics include: Self-Organizing Systems, Natural Selection, Dynamic Systems, Boolean Networks, Cellular Automata, Genetic Algorithms, and Evolutionary Robotics.
http://informatics.indiana.edu/rocha/alife.html

Amber ALife Wasps
Simulation of evolution by natural selection in a wasp population.
http://www.geocities.com/CapeCanaveral/2971/awasps.html

Darwin at Home
Planetwide effort to create networked digital ecosystems. Information on participating teams, how to get involved, and news.
http://darwinathome.com/