The only thing that actually kind of works for me is to bookmark stuff in "sessions" and then open the all tabs the next time I want to work on something. For instance I was trying something very specific involving deep learning at my job, then I had to do some actual work to prepare an article and I put that DL project aside. So, I make a bookmark folder with all the open tabs and closed the window. Now I got back to that DL experiment opened the all tabs again and that kind of worked for me. But this is not really a reference system, it's just a "sessions" system.
As for the traditional role of bookmarks, I don't think they will ever work for me without a single main thing: Full text search.
Every few months I try to clean the mess my bookmarks have become since I can't find what I need and a few months after everything is a mess again.
The tag or folder system simply just doesn't work for me, I keep too much stuff to check later as ideias and then I can't really find it because I have this folder "check later" where I have dozens of separate ideias and I can't really just find that one idea I had.
The solution seems to be some kind of full text search, where I can have a way to describe in a fuzzy way what I was doing, something like: "python, maps, names, germany" and go back to that post I remember where they where doing some analysis of the "last names of people in germany in different regions" and that I, of course, don't remember the name anymore.
I recon it's a very specific problem that only makes sense for people that think the same way like I do, but I'm also quite sure there are a lot of us like that and that this is the kind of solution that at least would help us a bit using the bookmark system.