I'm not entirely sure that these fall specifically under the 'donation' and 'digital initiative' categories that OP specified, but these are the institutions and pieces of software that offer their wares for free which I use often enough to give money to/purchase from.

- Octoprint

- Grayjay/Futo

- Internet Archive

- Opensubtitles

- The Guardian

I used to donate to Wikipedia, but for various reasons switched that donation to IA.