newdocms throws away the hierarchic nature of directory and subdirectory based filesystems, and implements a metadata system. It's pretty far advanced, and implemented for KDE. Check out the open and save dialogues. There's also a taxonomy feature, so searching for animals will find documents you've tagged as being about dogs. Neat.

See also: the Liquid File System, which can be sliced and diced along any file attribute axis. Bookkey implements this liquid system (screenshot) for browser bookmark management. [Links via nooface.]