BioKin Enzyme kinetic software.
BioQuest Metabolic Simulation
E-Cell From a Japanese group who have a modeling and simulation environment for biochemical and genetic processes for the Linux platform.
MetaModel Modeling Metabolic Pathways under MS-DOS
Pedro Mendes' Gepasi site, a popular bio/chemical simulator for Windows 32.
netBuilder A Windows based gene circuit simulator
DBSolve UK site Software for metabolic, enzymatic and receptor-ligand binding simulation.
Online Modeling System A web-based modeling system
JigCell Java based pathway simulator at Virginia tech (I know, two simulators in one university!)
bioSPICE DARPA funded biochemical pathway simulation software project.
Adam Arkin BioSpice etc
BioPathways “Supporting the Transformation of Genomic Information into a Web of Knowledge for the Life Sciences”
David Fell's Research Group Details of the research carried out by the group and links to software.
Princeton Integrative Genomics New institute dedicated to integrative genomics
Published StandardsCellML A corporate standard for storing metabolic type data destined for numerical simulation
BioPathways Consortium Corporate Sites
Entelos Company which specializes in physiological modelling.
KineCyte by Daniel Cook, a visual pathway simulator for the Mac (Commercial, but nice)
Gene Network Sciences Claims to be able to model very large systems