I just came across a food chain simulation by searching other people's bookmarks in delicious.com. Sunny Meadows provides an overview of the food chain, and then allows you to play a game to simulate what would happen "in the meadow" depending on how many predators, prey, and plants you decide to add. As the years tick by, you can watch as the population of animals increase and decrease based on their food supply. This is a great way to teach this concept. Even though the graphics leave much to be desired (see below), the idea is superb and so far its the only one I have found to illustrate this idea.
Here are a few other good food chain games:
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