John Holland's ECHO

Echo is a simulation tool developed to investigate mechanisms which regulate diversity and information-processing in systems comprised of many interacting adaptive agents, or complex adaptive systems (CAS).
http://www.santafe.edu/projects/echo/

Hardware Artificial Life (HAL)

Lotus Artificial Life's Java cellular automata substrate capable of supporting evolving, self-reproducing organisms which are capable of universal computation.
http://www.alife.co.uk/hal/index.html

The Swarm Simulation System

The Swarm Simulation System
http://www.santafe.edu/projects/swarm/

Gene Pool for Windows.

Gene Pool is an artificial life simulation where populations of physics-based organisms evolve over time.
http://www.ventrella.com/GenePool/gene_pool.html

Darwin Pond

An imaginary gene pool, a primordial puddle of genetic surprises. Free download; Windows.
http://www.ventrella.com/Darwin/darwin.html

E-den

Freeware artificial life program designed for Windows. 2-dimensional evolutionary world with simulated neurons.
http://www.geocities.com/ResearchTriangle/Forum/3830/

Java, Artificial Life, and creature behaviour

Java application simulates creature behaviours and movement. Available for free download, including source code, and a paper on Artificial Life.
http://skyscraper.fortunecity.com/altavista/819/

Critters

Agents evolve to stay on the screen.
http://www.oursland.net/projects/critters/

JuhasWorld

JuhasWorld: Yes it's alive! You have to see this applet to believe it. Just let those actors evolve for a few generations and they suddenly seem quite clever indeed. Wait a few more generations and you will be completely hooked: How good can they get?
http://www.geocities.com/SiliconValley/Bit/4699

Predators

Predators is an open-ended play-by-e-mail game. The game is an abstract simulation of animal species evolution.
http://perso.linuxfr.org/predator/

The Virtual FishTank

Designed for people of all ages, the FishTank offers firsthand experiences in creating artificial life forms and reveals how simple behavioral rules can produce complex and surprising results.
http://www.virtualfishtank.com/

NecroBones Artificial Life Experiments

Features three Java artificial life experiments.
http://www.necrobones.com/alife/

The MatremPage

An experiment in artificial life, and a game as well, where players create new animals to struggle and survive.
http://www.phys.uu.nl/~romans

Eden

A networked, self-generating artificial ecosystem by John McCormack. A CD-ROM version for Macintosh and Windows is available for on-line purchase.
http://www.csse.monash.edu.au/~jonmc/projects/eden.html

Genesis

A project being developed by David Stern at Cambridge university. Available in stand alone or '@home' flavours.
http://www.srcf.ucam.org/~dhs26/genesis_public/index.html

CoreLife

Implements an artificial-life environment based on - and compatible with - Tierra, Tom Ray's well-known project, which displays open-ended evolution using a world of assembly-language creatures running on simulated parallel processors.
http://www.xs4all.nl/~alife/corelife.htm

Red Bird Island: Artificial Life

Simple world with automata that act to form complex systems. Implimented on the Macintosh.
http://homepage.mac.com/redbird/brew/alife.html

Ant Farm Simulator

A VB based simulator of food-gathering behavior of ant colonies. Executable and VB source code are available.
http://www.geocities.com/chamonate/hormigas/antfarm

Quantum Flux: The Virtual Intelligence Matrix

A model of human brain function designed by a neuroscientist at UCSD. The VIM is used to drive 3D characters who live in virtual worlds and can express emotion and creativity.
http://www.qflux.net/

Pandamat

Highlights the Pandamat artificial intelligence system.
http://www.cswnet.com/~jwhitled/thesis.htm

Individual-Based Fish Modeling At Humboldt State University

Modeling software, theory, and applications. Instream flow model for trout. Salmon out-migration survival simulator.
http://www.humboldt.edu/~ecomodel/

PolyWorld Information (author's site)

Source of information, technical report, and source code for the PolyWorld computational ecology, maintained by Larry Yaeger, PolyWorld's author. (This site contains more up to date links and information than the PolyWorld page at the Santa Fe Institute
http://www.beanblossom.in.us/larryy/PolyWorld.html