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I'm a huge fan of Marvin [1]. It's an incredibly customizable tool that lets you create a ToDo app that works for you.
Unfortunately the web page doesn't make it clear how customizable it is, and how many unique features it has, but this may give you an idea [2].
[1] https://amazingmarvin.com/
[2] https://imgur.com/a/kPzzdko
MS to-do is my go-to. Multi platform and has all the features I need. Open source Linux option is “AO” on GitHub.
https://github.com/klaussinani/ao
For personal (non-work), I've been using a modified version of todo.txt (http://todotxt.org/) text-file format for over a year. My tweaks to it, and some helpful Emacs Lisp, is at: https://www.neilvandyke.org/todotxt/
For work project management, I'm recently using GitLab Issues and Board, with my own labels for urgency and Kanban state. (This isn't quite enough for large project planning, for which I usually use Gantt heavily. But hopefully the next time I need that, there'll be an easy way to link the work breakdown structure and dependencies to all the GitLab-based data capture and workflow the team is doing.)
That's nice, I generally like setups like this that capture content and give me control over things (I've seen something similar on HN with passively saving any papers in PDF format viewed in the browser and then building fulltext search on top if, or e.g. approaches like this: https://github.com/thesephist/monocle).
That being said, in the spirit of my comment — I honestly don't care too much about what I might be missing due to sites going down etc. anymore. The truly great stuff I save somewhere offline, but that's one or two levels past all the random things I currently use bookmarks for.
I think org-mode with org-roam[0] is what you're looking for.
[0]: https://github.com/org-roam/org-roam