I know wikis have been discussed here before, but I wanted to add my two cents after shopping around for a wiki at work and for personal use.

Obsidian

Pros

• plain text storage format
• great at gathering disorganized thoughts without imposing a rigid structure

Cons

• closed source
• many features that arguably define a wiki are either absent or paywalled, like easy sharing, collaboration, and versioning

Mediawiki

Pros

• it’s the wiki. Everyone’s used and possibly edited a Wikipedia page.
• version history
• close to Obsidian in terms of “write now, organize later”
• Probably the nicest-looking FOSS wiki platform out of the box
• a lot of the features that Obsidian paywalls are built in, like multi user support and version history

Cons

• Articles not stored in plain text
• Has its own markup. Granted Mediawiki predates Markdown but the table syntax is horrendous. The Mediawiki help page on the matter actually tries to dissuade you from using tables and notes that the markup is ugly.
• Extensions are annoying to install
• Absolutely zero access control. You can even edit other people’s user pages. There’s no way to hide sections of a wiki from the public or from particular groups of users.
• It tries to be all things to everyone. While this makes it versatile, it also means doing a particular thing probably requires knowledge of CSS or Mediawiki’s own templeting syntax. Sometimes I just want to have an info box that doesn’t clutter the source code of a page.

Dokuwiki

Pros

• Access control finally!
• Plain text files
• Easy to create namespaces, which Mediawiki also has but doesn’t want you to go crazy making your own.
• While it’s not Markdown, the markup is nicer than Mediawiki IMO. The table syntax at least is miles better

Cons

• Uglier than sin. Yes even many of the templates (themes) on offer aren’t much better. The Bootstrap 3 template seems particularly popular, and while it’s a marked improvement in most areas, like a lot of frontends that use those bootswatch pallets there are dusty corners that don’t work, like black text on a black background.
• Some stuff like tags and moving pages have to be achieved via plugins. Seriously you can’t even rename a page?
• Mutilates article titles. Makes everything lowercase and replaces non alphanumeric chars with underscores (or something else configurable).

Bookstack

Pros

• It looks good I guess. Haven’t spent much time with it.
• Yay markdown!
• Also has access control

Cons

• Also not plain text
• remember earlier when I talked about “write now, organize later”? Bookstack holds a gun to your head and forces you to use its shelf>book>chapter>page organization system. I know some people thrive under this limitation, but I don’t.

Other wikis I’ve tried but not to the same extent

Wiki.js

IDK, I don’t know much about this one, but don’t like the workflow of making new pages.

Gollum

Really simple, which is both good and bad.

An Otter Wiki (the article seems to be part of the name)

A lot like Gollum. Doesn’t indicate when you link to a nonexistent page. No support for article tags.

Pepperminty wiki

Looks cool but it’s abandoned

Tiddlywiki

Steep learning curve but pretty versatile. It’s a single HTML file so you can host it on something like Neocities. Really rudimentary search functions