Agent based simulation seems highly interesting for biological and/or molecular systems, which are too complex and "high dimensional" to be successfully simulated solely by mathematical means.
Stochastic simulation use to be the way to go then, but it seems agent based computing provide an even more general, and powerful paradigm for simulating this kind of systems.
In light of this, I was delighted to find Mason, a free (how does the "academic free licence" compare against LGPL etc.?) Java based software for agent based simulations, seemingly with many characteristics that make it good for integration in other software (Of course I'm pondering bioclipse integration here)
It seems to be quite working ... see the Conway's "Game Of Life" implementation, further down on the page :)
And, in case MASON is not the right answer to every question, they provide a shortlist of other interesting agent-based simulation software.