Enigma Encryption Simulator in Java
Component, CA, and CCA models; superdense time, DB repo, testing, etc.
Frevo is probably the simplest tool for evolutionary design
PySCeS Constraint Based Modelling
Small factory simulator for control logic test purpose
MC model of Endoscopic Optical Spectroscopy for tubular organ
LIME is a software tool for creating multiphysics simulation codes.