CJDNS (fc00::/8) is a friend-to-friend meshnet with end-to-end encryption that carries IPv6 traffic. Its aim is to replace the internet, perhaps preferably at the link-layer. It uses MPLS-like routing locally together with a DHT and floodfill for global routing. There is no built-in support for routing through other darknets, but it is possible to setup with a bit of bash-fu (e.g. onioncat or socat).
CJDNS is showing some problems with its capability to grow much further; connectivity is a problem for distant nodes. While the introduction of a floodfill mechanism is a remedy against this, it is probably only a cure of the symptom. A cure that is unsustainable for very large networks (maybe this limit has been hit already, even).
Meanwhile, CJDNS remains a somewhat suitable protocol for semi-automatic organization of otherwise chaotic networks. It works especially fine locally, as it can run directly on top of ethernet (thus making insecure protocols such as ARP or DHCP obsolete). Hackerspaces and other loosely organized groups could probably benefit from this.
Yggdrasil can probably scale better, although it have currently not yet grown as large. It is also somewhat more anon-friendly.
A partial map of CJDNS.