

Free Software Foundation Inc
The Free Software Foundation (FSF) is a nonprofit with a worldwide mission to promote computer user freedom.
Free software means that the users have the freedom to run, edit, contribute to, and share the software. Thus, free software is a matter of liberty, not price. We have been defending the rights of all software users for the past 39 years.
The Apache Software Foundation
ASF’s open source software is used ubiquitously around the world with more than 8,400 committers contributing to more than 320 active projects.
Software In The Public Interest Inc
The easiest method of donating to Debian is via Software in the Public Interest, a non-profit organization that holds assets in trust for Debian.

The FreeBSD Foundation
The FreeBSD Foundation is a 501(c)(3), US based, non-profit organization dedicated to supporting and promoting the FreeBSD Project and community worldwide. Funding comes from individual and corporate donations and is used to fund and manage projects, fund conferences and developer summits, and provide travel grants to FreeBSD developers.
Who doesn't love OpenZFS and the adorable little devil that brought it to us?

Zig Software Foundation Inc
Any chance to support a new low-level programming language that treads that middle ground between the total freedom (and lack of safety) of C, and the buckled-down regimen of Rust - count me in.
The Zig Foundation's Mission Statement:
"The mission of the Zig Software Foundation is to promote, protect, and advance the Zig programming language, to support and facilitate the growth of a diverse and international community of Zig programmers, and to provide education and guidance to students, teaching the next generation of programmers to be competent, ethical, and to hold each other to high standards."
Wikimedia Foundation Inc.
Likely one of the largest and most broadly impactful websites of shared, open-sourced knowledge, running under the Creative Commons license.
I suppose I should add - for those of us with nerdy kids who don't have a massive Encyclopedia Britannica collection available (do they even print them anymore?) - Wikipedia is a fun place for those nerdy kids to just peruse and read and learn random things...

Electronic Frontier Foundation Inc
Donate to the Electronic Frontier Foundation and support our mission to defend civil liberties and human rights online. You can help EFF’s attorneys, activists, and technologists protect privacy, free expression, and digital creativity at a time when the world needs it most.
Mozilla Foundation
Where would the 'Net be without Mozilla?