I have tried every variation of this, both personally and with clients, over the past 20 years. What I have found works best is a blended solution: use folders, but no more than about 20 -- specifically, no more than you can have fully expanded in the left sidebar of your email client. With this approach, you can still file them in the appropriate folder in about 2 seconds each (I agree that hunting through a collapsed tree is incredibly inefficient), but you can also organize around whatever key concepts work for you: clients, projects, reference, etc. I have found far too often that I couldn't find that one email because I couldn't figure out exactly how to look for it. My current personal organization, in addition to the GTD workflow folders, includes about 15 folders for active projects, a Reference folder with 3 subfolders, and one large archive. When the project finishes, everything in that folder gets dumped into the archive. Tl;dr: use folders, but no more than will fit on your screen.