For me, I use Orgmode, plus a mess of PDFs in folders on Google Drive. I've been looking into both Polar and Emacs as potential replacements for document organization.
Right now I have a single folder that I save new things to, and I have a recurring task to go back and file documents regularly. It's not perfect but it works. I don't often reference my pile of PDFs, though; I might use it more with tagging options, which is why I'm looking at replacements.
I used to use Evernote. There were some things I didn't like about it, although it's been so long that I couldn't tell you what they were anymore. It might be a good system now.