I use both dokuwik and, more recently, also wiki.JS.

Dokuwik is great and gets the job done but it's a piece of an old world. Maybe it's why I love it. Yes it's ugly and hard to theme. It's good old php all the way down.

Wiki.JS I love how consistent and easy it is to use and install. Has other drawbacks like require nodejs and store pages in a database, but uses markdown and feels modern and nice to use.