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!

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 loo 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.

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.