Matrix, which has some integration with Lemmy and is the default for secure chat amongst users here who need it.
XMPP, at least one Lemmy instance is also running it’s own XMPP instance.
Sup, which is explicitly pitched as a Fediverse Facebook Messenger replacement. Now Loops is launched and open source, plus dansup will get a bit chunk of funding via Kickstarter (so he can go full-time), it looks like Sup will be the next one off the production line and will be one to watch.
Signal is not federated, but I don’t know of an alternative. Matrix?