I've been toying with this idea but haven't had time to give it a shot yet:
I would, instead of creating multiple 'tier 1' stockpiles (stockpiles which give but don't take), hollow out the majority of an embark tile on a central z-level to be the One Pile, a 'tier 0' stockpile which accepts ALL goods. Other stockpiles must then ultimately take from there, either directly or from another pile which takes from the One Pile. (Refuse might have to be an exception if that designation causes rot as I've read before somewhere.)
This would lend a tremendous level of organization to dwarven inventory control. Problems with clutter accumulating on the floors due to full stockpiles would go away as the One Pile would serve as buffering capacity for all the others. Workshop stockpiles could be tweaked on the fly, knowing stuff you've disabled would have a place to go (ie if you wanted to make some cool nether cap beds for those hot summers, just disable all other wood in your carpenters pile and away it goes back to the One Pile). You would have to have two wood piles normally for this, one closer to the workshop taking the desired wood from the other; now the One Pile serves as that first pile for every workshop.
It would also be needlessly complex, labor intensive and time consuming. I'm wondering if anyone has tried this before or can see any downsides?