FlightGear Flight Simulator: free open-source multiplatform flight sim
Data manipulation and plotting program with scripting
Interactive geometry software for Euclidean and non-Euclidean spaces
PDBManip is a free program for editing PDB (Protein Data Bank) Files
A FDTD solver for electromagnetic wave simulations on a GPU cluster
NEVESIM is an event-driven neural simulation tool.
LIME is a software tool for creating multiphysics simulation codes.