Paparazzi is a free open source software package for Unmanned (Air) Vehicle Systems. For many years, the system has been used successfuly by hobbyists, universities and companies all over the world, ...
FlightGear - Usually for big airplanes, but can be paired with FC good description from PaparazziUAV or by Arduplane for simulation. AirSim - By Microsoft for algorithm testing. jMAVSim - For Mavlink.