One thing I love about the GMail label structure is that they are in fact labels and not folders. I.e. an email can be assigned multiple labels. That’s the case for how many other clients deal with their (admittedly wrongly declared) “folders”; You can set up a nested “folder” structure where emails can “exist” in many places. What it is is nothing other than labels in combination with a folder-like navigation scheme.
What I’m suggesting is simply to allow the assignment of multiple folders/labels (name whatever you want), and thus allowwing for more complex organisation of archived emails.