I think it was a donation system. But they were making some money off it so 🤷

Citra was free. It's only unfortunate collateral damage in the Yuzu switch emulator suit, since there was a lot of overlap between devs, and part of the settlement was that the Yuzu devs have to shut down all their emulation projects.

Yuzu was also free, but they ran a Patreon (reportedly taking in over a million dollars total) where you could get the early access builds for $7/mo. Most damningly, reportedly they distributed hotfixes to patrons run the ToTK leak before the game even released (i.e., before anyone could be hypothetically dumping their own legal copies to play). So a real triple blunder of taking money for an emulator, enabling piracy, and not maintaining even the veneer believing that people were only using it legally.

It should be noted that I don't think this is how the laws should be; I don't believe piracy meaningfully harms sales, nor do I believe it should be punished, but we have to be realistic about how things are; Yuzu would have lost in court, so we can only be glad they settled, rather than establishing legal precedent that would've decimated the emulation scene.

No, Citra was free. But the devs (same devs as Yuzu) had a Patreon where they were raking in upwards of $30k per month.

The software was free, but the Patreon gave early access to development builds. And when TOTK leaked a week or two early, the patreon’s popularity exploded because everyone suddenly wanted to be able to play the game on the most recent dev build.