This is a subject I seldom see addressed.
System designers had to compromise several factors when organizing the original Unix filesystem (cf hier). System files that were always loaded were placed together, then they started to spread apart (relying on the fact that computers are fast when they know where to look).
Sadly, my father organized our house this way. All pencils were in one drawer, all scissors in another. He ran about the house just to send a package, but he wasn't as fast as a computer. Even the Mac's interface is designed this way (Documents, Movies, Music, Pictures), though no one organizes an office according to the medium the information is stored on.
When asked once to design a computer system for a law office that could be used by temps immediately, I chose OS/2 to create a green desktop that represented the lawn outside, two doors (icons), one for the staff and a back door for me (pun intended). The doors led to the office's rooms (icons), desks, cabinets, tools (printers, &c). One ususally opened a client's folder, unless one had a new client. Then one opened the startionary cabinet and dragged & dropped (carried & placed) a template of a client's folder to the deskpad. In it were standard templates, to be taken to the typewriter, which simply edited the blanks. The filecases were two: open cases and close. The closed were folders sorted by name. The icons on the computer screen matched objects in the office, in appearance and relative location.
The MacOSX has some spiffy links called 'aliases': you can move the original without breaking the link. In any case, I keep Apple's arragement (except that I have a common 'Download' folder), but I otherwise organize by project.
A folder 'Mail to Grandmother' may have alias to Documents, Movies, Music, Pictures, and objects in any other 'standard' folder. Mac has helped by adding an optional column of little icons to their standard folders on the left of each folder you create. That way one can quickly open 'Pictures', grab the latests of Miffy, and close it again. My problems occur when I fail to attend to 'Downloads' nightly.
Office computers could be really easy to use, for offices are oganized. A home computer, as we've read, is another matter.