BitTorrent is not exactly a "messaging" protocol, but got immensely popular.
FireChat, a p2p messaging app, got very popular during protests in Romania. Sadly it's proprietary, so I'd stay far away from it.
Briar doesn't need any introduction in this group, methinks, but is not popular at all... yet.
But, messaging and e-mail are two different things. It's not just about sending the message. It's about the infra around it.