Where do you keep your messy stack of Markdown notes?

I keep mine in Obsidian - I have a 'rough' organization of notes, but search means I don't have to worry about it much.

They are mostly plain text, with dashes for the occasional list and a lot of deliberate indenting, so they are not "Markdown", which would slow down the note taking process too much.

I've had them in Notational Velocity, first as .txt files, then in the program's DB, since 2006, stored as .txt files in a "Notes" folder before that, and as a pile of "stickies" before that (not sure about the exact name but my default color was always light grey).

I don't synchronize them between machines because I only use one. I don't have them under version control because version control is not backup. I don't have them on a USB drive because they are not relevant when I don't use my computer. I don't use a hierarchy because it doesn't work well with informal notes. I only use tagging very lightly because the effort is not as rewarding as those old Lifehackers posts made you believe. And I back them up like the rest, though not as seriously as I should.

NV's search and general UX are awesome so whatever information I want to get out of those decades of notes is always a few keystrokes away.

(FWIW, the latest release of Notational Velocity was 13 years ago and still works like a charm after 11 major OS releases.)

Everything that doesn't need to be secure is in gitlab.com. When I used github.com I started a repository that I called "etudes" which were code and explanatory notes that went into a separate wiki repository. I used etudes for notes to myself and larger multipart explanations for others. After switching to gitlab.com, which doesn't really do wikis, I amalgamated code and notes into one repository and that works better.

For more secure information that I want to be more portable I use tiddlywiki on a USB stick.

https://en.m.wikipedia.org/wiki/TiddlyWiki

I wanted to like Joplin but it's not very fast. It takes like 5 seconds just to start.

So now I use: https://github.com/nuttyartist/notes

Logseq is great. Decent plugin ecosystem (but I confess being written in clojure is a major difficulty in the local ecosystem, even when most plugins aren't clojure).

I'm working to get the git-auto-commit program I wrote a couple years ago working again, to version control the history. There's now a git auto-commit built-in too, which I only noticed! Hopefully works well enough or is improvable enough for me!!

In https://www.inkdrop.app/ – no connection, but a big fan of it. The developer does some great screencasts of how he builds and uses it too.

Zim + Syncthing

https://zim-wiki.org/

https://syncthing.net/

In KeyPass. They are safe there, backed up, and searchable.

I use Joplin and I use Joplin Cloud for synch.