At the WikiSym conference in San Diego in October 2005, Ray and John joined forces with MarkDilley who had a much more comprehensive alphabetical wiki list of over 1000 wikis, called SwitchWiki. Mark had worked on SwitchWiki with others since 2003, and documented the ideas at MeatballWiki:OneBigWiki and WikiNodes Wiki:ProgressionofWikiOrganization
The three took the decision to join efforts together. The resulting wiki was to be more comprehensive and take full advantage of wiki technology. John converted and expanded the data from both sites and built out the original set of wikis in January of 2006. Throughout 2006 a community formed around WikiIndex and greatly expanded the number of wikis and improved the original format. By November 2006 the article count was at 3,195 and WikiIndex had become the authoritative source for information about Wiki sites.
WikiIndex dedicated volunteers include the following who have sysop status: Ray King, Mark Dilley, John Stanton, Ted Ernst, David Cary, Mattis Manzel and Sean Fennel. Many, have contributed significantly to WikiIndex in all kinds of capacities.
In January of 2007, WikiIndex.com switched over to WikiIndex.org, changed hosting from 1and1.com to DreamHost and upgraded to MediaWiki 1.8.2. In March of 2007, DreamHost experienced a server failure and was unable to restore WikiIndex and many other sites. WikiIndex was rebuilt back on 1and1.com on MediaWiki 1.9.3. In July 2007, we outgrew our shared hosting account and moved WikiIndex to a dedicated server, still on 1and1.com, and upgraded to MediaWiki version 1.10.1.
The number of wiki listed at the WikiIndex at various points in history is at the "How many wiki are listed here?" section of WikiIndex:FrequentlyAskedQuestions. (Should that section be moved here?)