I stumbled upon a relatively new fork of mutt recently called mutt-kz.
It is a project which was created with the purpose of modernizing mutt by heavily integrating notmuch, a fast mail indexer, into the client. This integration provides mutt-kz with the ability to have full-text searching, tagging, virtual folders, and more.
After compiling it and configuring the virtual folders and tags to my liking, I have to say that I am quite pleased with mutt-kz. It's now my defacto replacement for mutt on my machines.