Very often I think, how stupid these files and folders actually are. But I also think that Google Mail (with smart tagging and search), OSX (with an even better search, at least I'm faster with it) and Dropbox (automated versioning) already go in the right direction. I bet that some years later you don't have to worry about folders and files anymore.
I'm excited for auto-save and versions in Mac OS X Lion for this very reason: