PhpWiki is a WikiWikiWeb clone in PHP. A WikiWikiWeb is a site where anyone can edit the pages through an HTML form. Multiple storage backends, dynamic hyperlinking, themeable, scriptable by plugins, full authentication, ACL's.
Embeddable/J2E/Desktop Java Wiki CMS
WorkingWiki is a MediaWiki extension that makes a wiki into a source-code repository, IDE, and compute server. It has special support for LaTeX projects, including sophisticated translation to HTML for display within the wiki page.