QOwnNotes (QON) is a program for organising and syncing 'notes' / text files. By default it uses Markdown, but you can use plain ol' TXT files too. It can convert them to PDF and HTML (but the markup is a bit ugmo). It has built-in support for syncing to OwnCloud and NextCloud. You can pretty easily extend it's functionality with scripting. Styling the HTML previews is a pain for QT-related reasons!
I use it a lot!, and sync stuff between computers and my phone with Syncthing.
2020 Update: I feel like I would be better served by something else. I don't actually care about Markdown, so rarely look at the preview (except for tables). The main feature I like having is the list of all my notes on the left, and the easiness of searching and creating notes. Also the lack of support for todo.txt really bugs me. Still, I don't want to waste time searching for something new now.
2021 Update: Still using it daily. I don't use todo.txt, but do wish it handled not-markdown text files.
You can link to other notes by using note:// within a regular Markdown link, for example [link-text](note://note-you're-linking-to). You don't have to specify the folder it's in, if it's in one.
More recently the syntax <My note.md> / [Text](My note.md) | <My subfolder/My note.md> / [Text](My subfolder/My note.md) has been added.
You can insert HTML into Markdown; so you could, for example, add a <style> element with whichever rules you want, and wrap anything you want to gussy-up in html, use classes, whatever. Note the preview panel only supports a limited set of CSS (and HTML).
Noticed some new extensions to help with using QON as a personal wiki:
@:[tag] instead of just @[tag].