As for examples, I think ArchWiki is a great example of a successful “official” wiki, and EmacsWiki is an example of a successful “unofficial” wiki.
I don’t think the wiki in every GitHub repository will be enough for Atom. Atom is a very large and ambitious project (or a set of projects, like GNU), and GitHub wiki isn’t suitable for very large projects. AFAIK GitHub wiki doesn’t have effective spam prevention features (such as URL/word blacklist and CAPTCHAs), doesn’t support web feeds (RSS/Atom), automatic TOC, per-article discussion pages (although there are GitHub Issues and discuss.atom.io), watchlist etc. (But anyway, I like the “clone this wiki locally” feature.)