In the US, the EFF has been a long-time champion of freedom in the digital age. They're probably the most Snowden-esque nonprofit you can donate to, as they provide pro bono legal help in the defense of freedom in the digital realm (https://www.eff.org/pages/legal-assistance).

There's also the Wikimedia Foundation which has of course been responsible for the distribution of a lot of free information around the world.