Zotero appears conspicuously missing. It's an articles / references management tool. I've not found it especially useful myself, though it has its fans.
My own previous explorations, somewhat disorganised:
"Sources and tools for references, particularly document scanning and conversion"
https://old.reddit.com/r/dredmorbius/comments/6tr7za/sources...
"Organising and planning research activities"
https://ello.co/dredmorbius/post/fj5rzi8zmouyrmvg8yzzva
Regarding digital formats generally:
- Most formats are themelves opaque / resistant to annotations, in some way, shape, or form.
- Tools that enable annotations of one type of reference ... often don't support others. As several comments note, this results in various application or service-based silos of notes.
- Index cards remain remarkably useful. I use a modified POIC / Zettelkasten method:
https://ello.co/dredmorbius/post/u4dgr0tkxk4tk9npuvex5a
Mostly, I've been looking to a generalised system for organising and working with materials under the working titles of KFC (Krell Functional/Fine Context), docFS (as in "Document Filesystem"), and webFS (as in Web filesystem, see: "What if the Web was fileystem accessible" https://old.reddit.com/r/dredmorbius/comments/6bgowu/what_if...).
The idea of creating not an application, but an OS-level (and ultimately, hopefully, OS-agnostic) system for integrating metadata and relationships amongst documents, is at its heart.
This does seem like a surprisingly common problem, and one with numerous partial solutions, but no generally-available, general-purpose system seems to exist. Given that this notion dates back to (or before!) Vannevar Bush's Memex discussion, this is ... both surprising and disappointing.
I'm about 98.2331% certain that copyright has a major share of the blame, as an effective system for dealing with digitised documents would all but certainly have to involve duplicating and reverse-engineering them in multiple regards. My solution to the HTML / PDF / ePub, etc., document formats is to recompose them as some minimally sufficient document format (often Markdown, occasionally more advanced formats, with LaTeX being nearly always sufficient). This has resulted in a significant detour through questions concerning typography and just what a document is, though in a huge fraction of cases, there's little reason to go beyond paragraphs, the occasional italic/bold emphasis, and section or chapter markings.
In trying to decompose Web content, it's almost always simplest to simply dump the document to plain ASCII, then re-introduce any needed markup. Parsing HTML itself to a normalised form is a fool's errand. (As a fool, I've been on that errand many times.)
It's possible to start from raw ASCII text for a book-length work and re-introduce Markdown sufficient to create HTML, PDF, and ePub endpoints in an hour or so, for a fictional work with no significant typographic concerns. I've even resorted to hand-typing works on occasion. Excessive of itself, but with the added bonus of being an effective active-reading technique.
That said: none of my methods, nor those listed here, satisfy me.
Though Wallabag deserves a closer look.