For people who value full control and self hosting, Raneto looks like a good starting point to build from.
After having had to build knowledge bases in each company I worked in or go through the pain of implementing something bloated like Zendesk, I built a SaaS version of what I really wanted: the simplest knowledge base out there that stays out of your way.
Don't have Markdown support (yet) but we have a generous Free tier including custom domain (CNAME) support.