Being an architect, I'm used to dealing with thousands of documents on a project. The only meaningful way I've discovered to organize those documents is by the flow of work they are being used on, which is what we do. It is especially important when dealing with multiple companies on a single project. Folders and nested folders are a paradigm of the low-productivity windows way - we tried this, it never works well. But document management is really only a small feature of a larger integrated application that guides users through the larger workflow of getting projects done.