1. Roam by Roam Research
2. Zettelkasten there is a good book by Sönke Ahrens that covers the method in detail.
3. Org-Mode, a part of emacs. It's a text format is similar to Markdown plus a set of tools to operate on them.
4. Org-Roam, an emacs/org-mode version of Roam ([1] above)
5. Several Zettelkasten plug-ins for Org-mode.
Last year, I went down the emacs rabbit hole, because like you I wanted a better note taking system. I've been learning org-mode and emacs, but haven't yet circled back around to note taking and I can't vouch much for of the above suggestions.
Today, most of my notes are fleeting and need only to be stored on paper (and later thrown away). Everything else finds its way into an org file or flat text file.
I can say, that org-mode works even better than markdown with code. To the point that I am converting most of my linux config into one master org document, which gets parsed out into the various individual system config files.