coWiki: A content management tool with an intuitive markup language, unixlike access management, a directory structure and seamless page renaming.
FlexWiki: A wiki implementation that uses Microsoft's .NET technology (C# and ASP.NET) and has support for wiki namespaces.
GeboGebo - Wiki system: GeboGebo is an open source wiki system based on tdbengine. It is small, easy to set up and administrate and stores all data in a local, indexed database. It can optionally hold all content as static html pages, too.
OpenWiki: An IIS/ASP implementation with strong XML support.
Perspective: Open Source wiki engine, written in C#/XSLT, that supports WYSIWYG editing, file attachments, searching across pages and attachments (including MS Office documents) and a flexible security model.
Platypus Wiki: A Semantic WikiWikiWeb that uses RDF to manage metadata and ontologies.
RWiki: A Japanese WikiClone built using dRuby, ERb, RDtool, MutexM; inspired by Tiki.
SushiWiki: A wiki-like Web application running on .NET platforms. It is written in C#, uses ASP.NET features and stores data in SQL databases or flat XML files.
TiddlyWiki: An experimental microcontent WikiWikiWeb built by Jeremy Ruston. It's written in HTML and JavaScript to run on any browser without needing any serverside logic. It allows anyone to create self-contained hypertext documents that can be posted to any web server, or sent by email.
Vanilla: An extensible wiki engine written in REBOL, with weblog features and a streamlined interface.
Wiki Engines: Links to dozens of Wiki system types, in many programming languages.
WikiMatrix: A tool to compare the features of various popular wiki engines in comfortable side-by-side tables.
WikiWeb, Inc.: Commercial Windows-based implementation written in Smalltalk with limits on allowed named users, Access support, and ODBC support with more expensive versions.