Receiving materials from a classmate has made the issue of folder hierarchies more salient to me. In these comprehensive exam materials, articles are arranged by topic, which makes sense, but before that there is a dichotomous hierarchy imposed on the topics: industrial and organizational (I dislike this false distinction in my field, but that's another story). These higher order folders only have folders in them. This creates more drilling down every time I need to access articles. This creates the decision whether the topic I need is in "I" or "O." Then there are subfolders within topics, so I need to remember whether a topic is I or O AND whether it subsumed by another topic. This creates a lot of cognitive load.
Folder hierarchies seem to be a less and less relevant concept in modern computing, but they persist. Advanced searching and tagging obviate the need for deep folder hierarchies. Even rigorous files naming can help this when used with something like Spotlight. Though file browsers (Finder, Windows Explorer), still reinforce the folder paradigm AND duplicates for files. A better design would be a behind the scenes database design, like iTunes or iPhoto. Most people don't think about where their iTunes music is living in the File system, but it does keep it organized for transparency. I can imagine a Finder that more prominently brings in tags and "playlists" (smart or otherwise) that allow dynamic sorting of files without creating duplicates. I would only need one copy of articles that are used in a class, for the comp exam, and in my research. Hard drives are huge, but this would be more more efficient in space and organizing. A master database would manage this, as iTunes does, all behind the scenes. Tags, searching, and smart folders will create as needed organization without forcing the user to have to enforce and remember an organization. Everything will be searchable. The organization can be changed as often as needed. Finish the comp? Just remove the smart folder, but the files (and tags) are still there for later reference. Leopard's Finder does have smart folders based on Spotlight, but it's very limited and doesn't allow the kind of folder free organization I crave.
UPDATE: I guess this topic is in the air as the excellent UI blog, ignore the code, just posted on this topic. By the way, I love the recent redesign to his blog.