* PX4,
* ArduCopter (actually uses parts of PX4),
* PaparazziUAV.
These pack a lot of functionality: really advanced sensor fusion algorithms, position hold, waypoint/mission functionality, API for external control. At least PX4 has (working) integration with physics simulator (very useful for testing).All of them are great starting points if you want to develop additional useful functionality (e.g. package drop, autonomous mapping/patrol)- implementing even the bare minimum pitch/roll/yaw stabilization functionality takes a lot of effort.
The easier way to enter this domain is using an on-board/companion computer (typically RaspberryPi/Odroid) to control the autopilot using high-level commands (e.g. fly to these coordinates, activate that output etc).
Background: I have spent ~2 years working on (sadly) unreleased products in this domain.