I have never met a Confluence environment in the wild; overall user statistics I am aware of, and my personal experience, are that MW, Twiki, and Sharepoint dominate actual usage.
DoD uses it for Techipedia, which is a fairly large wiki:
http://gcn.com/articles/2009/10/12/gcn-awards-dodtechipedia-sidebar.aspx
I don't see why they didn't go the MediaWiki route, like Intellipedia though. I suspect they wanted ACLs.
Wikimedia uses confluence too (https://confluence.toolserver.org/pages/listpages-dirview.action?key=main). I found that funny when that was posted in another thread :).
MediaWiki isn't really designed to be an enterprise wiki, but it works fairly well as one given enough effort. Installing Semantic MediaWiki and associated extensions gives it a clear advantage over most enterprise wikis IMO.
Respectfully,
Ryan Lane