I’ve become used to using Zim, Cherrytree, and Joplin, for taking notes of various types. All have their pros and cons. My real concern is that notes are maintained in a format that’s readable in the long-term, regardless of applications that may appear in the future.
I don’t think markdown’s going anywhere anytime soon, what are your go-to apps or methods for taking notes?
I have moved all my notes from the various formats they were in to markdown.
Not only is it likely to not go away but even if it does for some bizarre reason, notes written in markdown are totally readable without a markdown viewer/editor so as long as ascii is still a thing I feel pretty good about it. 
Text files (.txt).
I don’t think text is going away anytime soon.
It’s ugly, but it’s reliable.
Zim just stores notes in text files IIRC, but you can sort them hierarchically in the Zim GUI for better organisation.
As dumb as it sounds my one way of taking notes just to write in a text file using mousepad. I do use indent dashes and etc. Text files will always be around forever and are very light.
I write markdown in a text editor (Kate). Most of the time, I don’t even bother looking at it with a markdown viewer, but if I do, I use Okular, not because it is particularly good, but because I already have it installed and can’t be bothered with anything else. 
Markdown is never going away. It may become less popular, if something better takes its place, but markdown parsers are trivially simple and will always be around.
I write my notes in org-mode in emacs, a simple, readable syntax, with the ability to write equations in LaTeX. In addition, the files are nothing more than simple text files and therefore very simple to keep and synchronize with git. Badly, it converts everything to markdown with one command
Visual studio code (package code) can edit markdown nicely and also has a built-in viewer for it.
Usually I’m using it for writing markdown.
I’m using Joplin - I have typora for a notepad which is good - some things just sit in a folder so the notes are all safe, Joplin is great, but the file naming can be a problem if I make a lot of notes and stop using Joplin… but it’s good for taking notes and reading them in my ipad because they’re synchronised via the evil Dropbox.
Works good long-term
In the end I’ve decided to stick with Zim, - with the files being stored as .txt with a clear format and hierarchy as you said, I can essentially edit them in any editor, CLI or otherwise, and they’re just as readable. Sometimes the simplest solution is the one you’re already using…
In the last four years I’ve used quite satisfactorily Cherrytree. If need be, it has good import and export facilities. It can provide your notes with a minimal but handy protection.
I’m using Zettlr, mainly because it has zettelkasten prefixes and I use it for naming all my files.
Now that I have installed KDE and not removed Gnome yet, because it breaks my browser syncing and Deja Dup, I am ready to give Kate a try.
Someone posted a really nice primer on Kate, but I can’t remember who posted it or its title. Do you happen to know what I referring to?
Michael
Sure, Kate is very nice.
I keep my notes in a separate documents folder - the upside of this is that they also work very nicely in Obsidian (which is brilliant for linking them and my favourite for creating notes with lots of cross-references, links and back-links).
Mark Text gets top marks for the way it looks - sleek and clean (similar to Typora) and for the single type/preview window (and MarkText can be set as the default editor for your Joplin or Obsidian notes - though the links made in Obsidian only work in Obsidian).
I’d definitely recommend giving Obsidian a whirl - it creates simple .md files, so (unlike Joplin) there’s no issue with the notes being readable, but there is an issue with the links outside Obsidian if you do it the Obsidian way…
Plasma just became my DE after finding Gnome too rigid. KDE gives me Kate, which I have so far found to be a powerful productivity tool when integrated with Krusader.
But when it comes to storing your notes with bi-directional links, IMHO it’s pretty hard to beat Obsidian. (but it’s closed source if that bothers you).
Michael
As a side note I chatted with the developer of Joplin and he does not have much interest in back links.
I have used Obsidian, Joplin, Standard Notes and Simple notes in the past, but have settled with Logseq as I find it on par with, if not better than Obsidian. Logseq is also open source, which Obsidian is not.
For me, Joplin was the only thing I could find that met all my needs:
I should probably check to see if anything else has popped up in the last couple of years that is better.
But I want the notes to be linkable and as powerful and highly configurable Kate is, it is not bi-directionally linked as far as I know, and that is what you need in the long-term. As our notes get older, we as humans, tend to forget obscure but relevant connections we have already made years before. So having this feature lets us rediscover and ink our research.
But as far as a PKB (personal knowledge base), i’m with you on this @Ben which is in the AUR as an AppImage
I also like Zettlr, as they both read the markdown files and use [Zettelkasten] (https://zettelkasten.de/posts/add-identity/) prefixing and Obsidian has a switch in configurations and Zettlr is by default. I chatted with the founder of Joplin and he did not express much interest in bi-directional links or Zettelkasten.
Zettlr is for academics needing citation for their theses, but I use it for as a PKB, which I integrate with Pandoc and Zotero for connecting to citations.
Michael
I like that term Digital Garden. Thanks for the link. The one thing about Obsidian that bothers many including me, is that it is closed source.
Michael