So, there's already plenty of "shadow" activity on the internet, such as hacking, data piracy, etc.

But check this out, 'Darknet'.

The end of the article makes some good points about how the servers can't be totally anonymous, however, what's the difficult in setting up your own "Darknet" vpn?

edit: After checkingWikipedia, it seems that truly anonymous VPNs on wireless networks face some hurdles... but that makes me wonder "just how does the government keep all their communications private?"

Encryption.

And, yeah, I suspect that there have been such things for a long time relying heavily on secrecy and palimpsets.