DokuWiki - DokuWiki is a simple to use and highly versatile Open Source wiki software that doesn't require a database.
HowHive - Knowledgebases for teams and companies of all sizes. Knowledge sharing and finding made simple.
Wiki.js - An open source, modern and powerful wiki app built on Node.js, Git, and Markdown.
Raneto - Open source, flat-file Knowledgebase platform that uses static Markdown files
TiddlyWiki - a non-linear personal web notebook
openKB - openKB is a Markdown Knowledge base application (FAQ) built with Nodejs and ExpressJS.