Instead of folders, if you think of the Tags in the same way that gmail has Labels then you can tag any of your object with preset tags, or create new ones on the fly.
When you want to hunt down just objects (we'll say Files) in a certain "Folder" you just go to the "All" workspace, click on the Documents Tab and then click on your "Folder Name" in the Tags Panel.
Edit: And I just thought of something, objects can have multiple tags, while a file can only go in one folder, so you would have to know where to look.