1) I collect a bunch of Very Important Documents and Files. I maybe try to organize them.
2) At some point (days in...) this falls apart.
3) I get sick of not being able to find new files and throw everything in some folder ('archive', 'shit', whatever)
4) these end up on a hard drive in a drawer somewhere, eventually.
5) I go "man I need to throw away these old hard drives, better make sure there's nothing good on them"
6) I find the junk folders go "oh man good thing I didn't just toss this drive" and put the junk folders somewhere on whatever my current backup/mass-storage drive is ("uhhhh I don't have a good place for it, I'll just stick it here and go through it later to categorize everything, I'll just call this 'old_drive_stuff'" but of course I never look at it again).
7) At no point do I examine or use any files that land in any junk folder aside from maybe getting a brief "oh shit I remember that!" nostalgia trip on re-discovering them, before tucking them away again, not to be seen until I am once more clearing off an old hard drive so I can throw it away.
Incidentally, I think two things that might help with this are 1) not having to manually clean up filenames and metadata on every goddamn thing before I feel comfortable putting it in with my "nice" files (this is part of why files accumulate in a kind of "junk drawer", because I put off this work), and 2) some kind of easy "send-to" workflow to toss (especially downloaded) files to pre-defined categorized locations, ideally with both a very quick manual interface (not farther than two clicks away, or one CLI command) and an optional automatic one based on file extension. All configurable, naturally. Bonus for more complex filtering rules—like my mail inbox, really. Yeah I could write it but that's one more thing to carry around and another thing that would leave me helpless on machines that aren't mine, or aren't my main OS, or whatever. It should be built into the OS or file manager.
I also think there are lots of different kinds of files and handling them all the same isn't great. Ideally my editing-format documents would actually be a container holding an archive of "finished" versions of them (not just every time I've hit save, and certainly not a complete undo history or anything) so they all move around together and can't get separated. Same for photos, probably—keep an original and any edited variants I've made all in one file and only (and automatically) split them up (export one of them) when it makes sense to do so.
[EDIT] example of otherwise-good software that tries to do some of this organization for me on-file-open but fails at it: iBooks. There are two main categories of ebooks I open: those I want to keep around permanently, and those I just want to look at for a little while then I don't need it anymore, or that I want to keep around but strictly associated with some other files on disk. Opening a .epub adds it to my icloud-backed-up iBooks library every single time. This is perfect for books I want to keep but sucks for books I'm just opening for a second, because then I have to go delete them, or keep a second (probably worse) ebook reader around and understand both programs' features. I have two types of .epub, then, with different use cases and organizational patterns needed—I need an "add to library?" prompt when I open them. IIRC Calibre does something similar and can't be my only ebook reader for the same reason (which makes me want it not to be an ebook reader at all, just an organizer accessible through an open-with menu)
[EDIT 2] Oh it's just called "Books" I guess. Was it ever iBooks or did I imagine that? Whatever, point stands.