Yes, this is what I do, too. But sometimes I just forget stuff is in the folders. It gets a bit cluttered as the kids get older and I collect more stuff, so then I create subfolders. But it seems like the more levels down I go, the easier it is to forget about things.
Also, I can't figure out how to make this work for things that are streamable with nothing downloaded. How do I remember that I have access to a video course on some random website where I have nothing else, and there is no downloadable component?
I need to figure out how to organize a megalist, I think.
I have a folder in my bookmark list that is named Homeschool. I then further divided that folder using the same system as I use for my homeschool directory. Personally, I do it by age, so if I download a science resource meant primarily for elementary, then I file it under Science - Elem.
If I want to save a similar streaming resource then I bookmark that in Science - Elem. THEN, and this is the important part, I go into the Science - Elem. folder in my homeschool directory and I create an empty folder named something that will remind me about the streaming resource. So I end up with an empty folder named Interactive Solar System or whatever.
Later when I am looking for astronomy resources, I open that empty folder, realize it is empty and therefore just a reminder, and I know to go to my bookmark list and find the link for the Interactive Solar System.