Netsukuku is anonymous, while cjdns is not; cjdns uses an unused IPv6 block for addressing, netsukuku has its own addressing thing; cjdns has a very clever end-to-end encryption scheme, I'm not sure about netsukuku; netsukuku has fun Lain references on its website.
I've never heard of netsukuku until now, but from a quick glance, they are very similar except that cjdns has a much higher usage in the wild and doesnt have an answer to dns.
