I currently use [[logseq]] for taking notes and storing fragments; and [[hypothesis]] for annotating the web and pdfs hosted online. but I use both on desktop only — on mobile I don’t have either note taking or annotations solved. I mostly go to anagora.org/<node> on a mobile browser and write things down in the stoa (shared document) when pressed.
[[logseq]] is agpl and it’s almost as good, but outline-oriented; meaning you get a bullet-points-first UI. it has a document mode though, and supports both markdown and org mode as formats.