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.
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.
It seems crazy, but it may not be more intuitive for some other people. :)
I suppose you could mix the Windows 8 approach (all groups) with iOS-esque folders, and allow subfolders, and then you have the best of both worlds.
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.
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.