I've worked with MediaWiki, DokuWiki and contributed to an add-on for SMF that was aspiring to be a functional wiki (some builds were usable over time, but it discontinued as the original author moved on)
MediaWiki is actually a colossal pain to do anything with; fixing up the login to use the forum login isn't particularly hard (SMF, at least, has a bridge for this) but it's more annoying to skin than almost any other software I know, and I dislike a lot of things MW does at a fundamental level; the Talk pages are probably the worst feature in my head, it's the pinnacle of 'all I have is a hammer, every problem looks like a nail', in lieu of a real commenting system. And that's before we get into how twitchy a lot of MW really is to use, the markup feels more flaky than bbcode ever did.
DokuWiki has different problems - bridging the auth is slightly more awkward than MW's, but it doesn't use a database, everything's in files on disk. While that has some technical advantages, it makes it annoyingly hard to do any nice integration back into the forum, e.g. in widgets or blocks to showcase wiki information in the forum.
Naturally, having these things as external systems also raises drama around other kinds of integration - linking from forum posts to wiki posts feels disjointed because it *is* disjointed. Ideally it should be as seamless as linking to a wiki post from any other wiki post, but this is the same problem as having a gallery or articles system: you're bolting it on the side and you really need to do something smarter and cohesive.
I'm actually going to be adding a native wiki to my forum platform once I finish up where I'm currently at - but it's for roleplay purposes, so chances are it won't be useful for most cases, though I plan on doing a bunch of things that are very cohesive around connecting the two - I need it for all the lore and fluff about the roleplay world I have, and I figure if I need it, chances are other people will too.