Just a few other (older) examples - Gore-tex (WL Gore), Patagonia and Semco have had structures that could be described as self-organizing or "flat". 3M is another example.
If you want to learn about Semco, make sure you read "The Seven Day Weekend", not just "Maverick!", since the former gives an updated view of the business from 2004 or so.
Would be interesting to see what Semco looks like today - probably nothing like what it was in 2004.
An important aspect of the organizations you mention that isn't mentioned in the article is explicit profit sharing and co-ownership, not just options.
This is a feature that seems fairly at odds with the desires of VCs who often seem to do everything they can to dilute workers options pools. And also with wider investment market who often see employee ownership as a threat to the value of their investment capital.
Edit: Another one that I reference, Automattic.