AMMDI is an open-notebook hypertext writing experiment, authored by Mike Travers aka mtraven. It's a work in progress and some parts are more polished than others. Comments welcome! More.
Agar had a somewhat more sophisticated modelling framework for behavioral rules, inspired mostly by Tinbergen's ethological theories. (built for my master's degree)
The Electric Anthill was an exhibit I built for the SIGGRAPH Art Show in 1989, based on the software I was working on at the time for my MS thesis, Agar. It was interactive, which was not that common at that time and place. It had a screen with ome artificial ants. You could drop food with the mouse and they would find it and make navigation trails for the colony. Seems kind of trivial now, but I guess it was interesting at the time.
Agar is a system I built as part of my SM degree work at the Media Lab. It provided a set of objects (world, creatures, sensors, actions, and behaviors) for creating simulations of animal behavior. The behaviors are specified in terms of agents, or small units of behavior. Agar's main example was a simulation of ant food-foraging behavior.
The best description of Agar is in my MS Thesis, Agar: An Animal Construction Kit) (1988). Unfortunately this version does not have illustrations.
Agar was written in an ancient version of Mac Common Lisp, the Lisp source is available but probably not runnable without a ton of work. There's also a runnable application which again, won't be of current use, unless you find an emulator that works.
Agar's notable distinctions include:
Winning the prize for "best software insect" at the 2nd Workshop on Artificial Life, 1990.