Ardupilot -- Ardupilot is a popular platform for controlling drones and is a good way to get started with autonomy.
PX4 -- autonomy platform that provides easy extensibility for developers.
Control Interface
Mission Planner is Ardupilot's primary tool for communicating with devices in the field.
Ardupilot methodic configurator -- Methodic Configurator simplifies the process of finding the best configuration for a particular set of hardware.
QGC -- A nice field control interface to plan and execute flights. It includes a toolbox of utilities to check the logs of various subsystems, configure custom variables and calibrate your hardware.