Webworld
Webworld is a food web building algorithm published by Drossel, Higgs and McKane (2001). Alan McKane's website has papers and information about the original algorithm.
In late 2005, I reimplemented the Webworld algorithm and added a few extra bits and pieces to study the role of evolution and invasion in structuring webs and determining their invasibility. Some preliminary results were presented at CSIRO's Symposium Strangers in Paradise: Invasive species as cause and consequence of evolution.
In 2008 I prepared a manuscript on the food web attributes that mediate the relationship between species richness and invasibility. It's being reviewed right now, so I can't put a copy of the text online. Please email me if you would like a copy of the latest draft. Alternatively, you can download a talk I presented on the same topic at the Mathematical Models in Evolution and Ecology Conference 2007.