Notes, once entered, must be processed. The best way to process them is to write them away into the projects where they belong. The worse way is to file them in some limbo folders.
Provisional filing may be needed from time to time, more precisely from space to space. The need goes from work urgency to artful time waste management. Too much files in a folder seems both ugly and wrong.
Besides, default folders are almost always inconsistent. Music, pictures, and videos are sometimes downloaded ; they always are documents. Are pictures the same thing as images ? Projects can have all kinds of documents anyway.
The real problem concerns the files outside projects. So let them be projects of their own. Projects come in three flavours : done (out, old), urgent (now), wish-I-was-Superman (maybe). These modalities are related to the time of need : past, present, and future.
The mind seems well attuned to this triumvirate. The Past, even the rewritable one, contains all that has expired. The Present encompasses the very near next. The Future always comes by while always remaining the worlds of possibilities.
Seeking the ultimate organization can be as essential as futile. But the constructive systematization of one's own work entails both simplicity and beauty. Only love can save a filesystem from entropy.
Addenda. ~~ Since the Desktop is for Now and the Archives are for Old stuff, then there is only one folder to add : Maybe. Coloring the files so that they are recognized as urgent, interesting or dealt with can improve the correctness of the scheme. Folder actions could also automatize categorization.