With FlightGear it is possible to choose between three primary Flight Dynamics Models. It is possible to add new dynamics models or even interface to external "proprietary" flight dynamics models:
JSBSim: JSBSim is a generic, 6DoF flight dynamics model for simulating the motion of flight vehicles. It is written in C++. JSBSim can be run in a standalone mode for batch runs, or it can be the driver for a larger simulation program that includes a visuals subsystem (such as FlightGear.) In both cases, aircraft are modeled in an XML configuration file, where the mass properties, aerodynamic and flight control properties are all defined.
YASim: This FDM is an integrated part of FlightGear and uses a different approach than JSBSim by simulating the effect of the airflow on the different parts of an aircraft. The advantage of this approach is that it is possible to perform the simulation based on geometry and mass information combined with more commonly available performance numbers for an aircraft. This allows for quickly constructing a plausibly behaving aircraft that matches published performance numbers without requiring all the traditional aerodynamic test data.
UIUC: This FDM is based on LaRCsim originally written by the NASA. UIUC extends the code by allowing aircraft configuration files instead and by adding code for simulation of aircraft under icing conditions.