Currently I’m using Joplin with Syncthing-backed file system synchronization. I’m pretty pleased with it, as I do like tagging- and Markdown-based systems.
I plan to upgrade to server-based synchronization, but before doing that, however, I wanted to see what other people are using.
Edit: So far I see a slight favor towards Joplin and Logseq, but I totally didn’t expect (and appreciate) getting so many different answers.
Handling PDFs and being able to use a pen is the one reason why I still use GoodNotes on the iPad for everything. To make it semi-searchable I use a filesystem on my server.
I have several active GoodNotes documents for my notes, calendar and work. And my own index document for all the other documents lol.
It feels like the stoneages when comparing it with the nice features programs like Obsidian or Joplin offer. But none of these programs work with PDFs and handwritten notes/annotations.