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JSBSim
JSBSim is an open source flight dynamics model (FDM) that provides a high-fidelity model for a wide variety of aircraft types. It is used in many aerospace and aviation applications for flight simulation and analysis.
X-Plane
X-Plane is incredibly extensible. You can simulate new aircraft, make 3-D models, or even change the functionality of the program in drastic ways.
FlightGear
FlightGear is an open-source flight simulator that offers a highly realistic flying experience. With a global community of users and developers, FlightGear is constantly being updated and improved to provide the most authentic flight simulation possible.