Here are a couple of the former:
RTEMS https://www.rtems.org/ Core Flight System (cFS) https://github.com/nasa/cFS
NASA has a lot of open source projects including a bunch that don't "go to space" but are used in space related projects (check each project for contributor guidelines):
https://github.com/nasa/openmct - web based mission control software https://github.com/nasa/trick - simulation for for all phases of space vehicle development
You should check out their github organization for all available projects (https://github.com/nasa).
Also, European things as well such as the ESA's github organization: https://github.com/esa, and Germany's DLR: https://github.com/DLR-SC.
Another good group to check out is TU Delft: https://github.com/tudelft, https://github.com/tudelft-iv and others.
Not to mention a bunch of open source CFD projects on github that are widely used and other similar tools. Again, not strictly software that goes to space, but you will find more of that too if you search for projects related to those mentioned above.
I wonder if SpaceX will publish some of their tools to the public in the near future.
Open MCT code repository: https://github.com/nasa/openmct/
Original pull request: https://github.com/nasa/openmct/pull/1146
Video of the plugin in action, pulling telemetry data into Open MCT: http://quick.as/9wZiOe5d