Normally I only use Zim. It fits perfectly for me, because I need the documents in markdown format.

I use notion, mindly, transno and Emacs to write

I use Manuskript, which is a pretty nice FOSS writing program. It lets you define a whole encyclopedia about all aspects of your story (characters, locations, magic, technology, etc.) and breaks the whole thing up into scenes that can be reordered at will, put into folders to create larger sections (chapters, or even sub-chapters), etc. And, when you’re done, you can have it export the project (any/all of it as you wish) to just about any format: text, Word, PDF, whatever.

I’ve also been toying around a bit with Obsidian. It’s not really meant as a writing app, but you can definitely do deep outlines as well as all of the same type of encyclopedia/wiki setup to help you keep track of everything.

I use scrivener. What I love is that I can write scene by scene and also have a place to store notes and such.

I’ve also tried a free alternative: novelwriter, and really liked it. I can do certain things easier in Scrivener, so I went back 😃

I use Obsidian for just about everything related to writing. I like it because I can stash every little idea and scrap of scene I have about a WIP in one connected folder to rework and drop in on the fly. Plus, it’s cool to see the graph grow with a project.

I would have a look at Manuskript.

However, I tend to write with whatever’s in front of me. Currently using WordGrinder for one thing, Joplin for another, and Pages '09 on my sixteen-year-old MacBook.

Yeah, I’m using Scrivener. Before that, yWriter, basically a clone with less features, but free. Loving them both, even though I’m only using Scrivener these days.

To be honest, I just stick to plain ol’ LibreOffice. I use folders to organize notes, which isn’t perfect but works for me.