vimwiki
combined with some bash aliases, neovim config tweaks, and some bash scripts I've cobbled together over time. Then syncthing to share it across my laptop and desktop.
I've tried a few different note taking apps but I always find myself coming back to vimwiki. Its not the most feature rich 'app'. Matter of fact its pretty simplistic but I dont need or want most of the advanced features of other notetaking systems. But what it lacks in features, it makes up for by being a vim plugin. Seriously, I can't handle using non-neovim text editors/note taking apps. Having all of my neovim plugins, and other config tweaks make vimwiki the handsdown winner over the rest.
The missing vimwiki feature for me was a running "to do list" across all of my notes. So I wrote a script that got me the to-do list feature I needed.