I'm not sure what sort of workflow and mail client you desire, but Notmuch supports arbitrary tagging. Most coverage I've seen of it integrates with emacs or mutt (or similar text-based mail clients). That said, in searching for the project homepage, I also saw this project[1], which might be interesting if you're looking for something a bit less terminal. I'm sure there are more alternatives, but hopefully this is useful as a starting point for you.
(Sadly, my workflow is heavily dependent on multiple labels per email, and no IMAP client seems to work acceptably in that situation.)