MONOD: Modeler's Notebook & Datastore. MONOD is a web-based framework that allows many researchers to help build and analyze models of biological systems.
Stochastirator: An accelerated discrete reaction event simulator (available here). Stochastirator is a C++ implementation of a Gibson-modified Gillespie algorithm for computing the time-dependent behavior of coupled sets of chemical reactions. A version that compiles on Mac OS 10.2 and other machines (fixed namespace/header issues) is available here.
TABASCO: A single molecule base-pair resolved gene expression simulator.