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Well that's what is usually is associated with, so naturally that's what came first into my mind. This is their transport https://github.com/berty/go-libp2p-tor-transport which is a transport layer for libp2p over tor, so you can reach any peer by their multihash by first going through tor network. Quote: "Annonymity, this will works like you expect 3 hop tunnels, in combination with a correct configuration of your libp2p node you will be able to also dial non annonym nodes through an exit relay.". Not sure if it has anything to do with onion services at all.
https://ricochet.im/ is an p2p instant messaging system where both parties run servers to exchange end-to-end encrypted messaging. Same goes for https://briarproject.org/ and https://cwtch.im/ and https://github.com/maqp/tfc (my personal project).
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