WikiEngines that uses MySQL, generally combined with PHP
CockatooWiki -- is simple PHP/MySQL-based wiki solution. Aims toward easy setup and customization.
CoTeia -- XML-based Brazilian collaborative authoring tool with access control (optional), concurrency control (WebDAV), chat server, annotation server and site map. Runs on MySQL. Seems to be Swiki (SimpleWiki).
coWiki -- follows the tradition of loose wikis with easy and intuitional markup, adding Unixlike access management, a directory/document hierarchy, and a plugin API for your functionalities and enhancements. All documents are parsed to XML for further export and transformation. coWiki is modular, template-based and multilingual. Requires PHP5 and MySQL
ErfurtWiki -- embeddable into existing sites, uses SQL or flat-file backend, single script, allows plugins.
PWiki2 -- a PHP+MySQL based wiki with file uploading, NameSpaces, DynamicFunctions and more.
sfWiki -- also uses MySQL; designed for SourceForge sites.
WakkaWiki -- very smallish PHP/MySQL Wiki with quick installation, access control through per-page access control lists, full revision control and page comments.
WikiTypeFramework -- PHP/MySQL collaborative Web development system.
wikiX -- PHP/MySQL-based wiki. It aims to allow users to redefine syntax by using wikiXmacros and various stages of PHP plugin.
