Agent-based simulation toolkit
Draw and Simulate Finite States Machines (FSM)
OpenNum lets you distribute solvers with a nice graphical interface
A wireless push-type network simulator.
NMR Product Operator Calculator
Modbus slave simulator
Quadrotor control, path planning and trajectory optimization
A C++ Matrix Library
A simulator for biological and physiological models
Portable OS X FOSS applications
Antimony is a human-readable, human-writable model definition language
PySCeS Constraint Based Modelling
Biomolecular electrostatics software