Little note: Maybe it's my browser, but I just see the words "Image Image" in your spoiler.
Back on topic, thank you for starting this thread. This is a major problem for me, and I'm interested to hear other people's ideas. I definitely do the too-many-folders thing, so the LJ thread you posted was interesting to me. I'll have to think of how I want to restructure it. I also wish I knew a good way to organize old stuff that wasn't originally organized well - like most of it is junk, but I want to keep some of the stuff and I'm not sure how to find meshes for files, group things, completely delete things, etc. If that's too far off the original topic, please ignore, but that's another thing I worry about.
Anyway, hoping people have some good suggestions. I, unfortunately, don't - my newer downloads are in sub-folder hell, and my older downloads are a frightening mishmash. I'm a mess when it comes to downloads, basically.