Matrix I have doubts about. The idea of Tox was nicer, but the implementation quality and the scandal at some point didn’t help.
Tox felt more playable, like piping files over it or a remote shell over it (I know, bad associations, but still), or even using it for VPN. I think there were clients allowing to do such stuff, and the protocol allows it.
EDIT: I mean, it’s still alive, just don’t see it claiming the place of FOSS old Skype replacement as it did.
GNUNet - all you people mentioning it have peers? I tried to set it up a few weeks ago, couldn’t get peers.