Wikipedia - While the Wikimedia Foundation itself is hierarchical, it manages Wikipedia through a process of community-led governance. Every article is maintained by a community of volunteers who engage in open debate to decide on content moderation policies. Wikipedia remains one of the few popular websites to avoid the recent internet enshittification.

Food Not Bombs - An activist organization that serves free food. FNB has no central organizing body, instead operating as a loose-knit group of independent collectives who voluntarily cooperate and exchange information and resources with one another. One specific collective, "A Food Not Bombs Menu," has taken to coordinating the global activities of FNB collectives and helping people start new ones, but has no power over any others.

IWW - The Industrial Workers of the World, while hierarchical, ensures a hierarchy that is accountable to its' rank and file members by means of a robust democratic process, as well as the right of any member union or individual member to leave at anytime and go it alone.

There are many more, but it's late and it took me a while to pick out what I think are good representative examples of different ways an organization can be run well.