Hmm. Homescreens seem to work well enough for organisation of apps, better than start menu folders anyway. Perhaps file "grids" instead of the traditional hierarchy of folders might work better.
I used to be of the mindset to keep a clean desktop, then I came to my senses and used it as a working space. It's easy to get to from anywhere in the OS as it generally has it's own shortcut'd location. Temporary working files just get stored there. Permanent files might have a shortcut to them stored there instead, leaving the real file in a more suitable location. The 'ugliness' associated with such a desktop is meaningless once I realised most of the time the desktop is covered.
The most infuriating thing about Gnome 3 is that it decides for you that the desktop is an unholy place to keep anything, because you're too stupid to figure out how to do things efficiently.
It seems crazy, but it may be more intuitive for some people. People often use muscle and visual memory to remember where things are, not necessarily by name of location.
Edit: Plus, you can always add naming and search with it. And Microsoft has an interesting grouping concept in Windows 8 with grouped and optionally named sections, not folders.
Doesn't seem crazy to me at all. It works well for that use case, but it doesn't scale well to hundreds of entries.
Once you get into groupings you're creating the same problems that people have with filesystems (implicit or explicit organization challenges, loss of discoverability, etc).
Search (or something like what we call "search" today) might be the best step forward from here, but you can layer that on top of any other (or no specified) KV metaphor you like.
They may be a tolerable layout for your set of apps, which tends to be pretty small, but for organizing all your files it quickly becomes a giant mess.
