TightVNC appears to support IPv6: http://jungla.dit.upm.es/~acosta/paginas/vncIPv6.html
Not sure about the other VNC implementations.
As for IPv6 tunnels, etc, you really have to figure out what the firewall allows. If they allow SSH in, you could probably establish a remote desktop via the various SSH tunnels. If the firewall allows IP proto 41 out, you could establish a 6in4 tunnel to your remote box. You could also use SSH to have a remote box listen and relay into your inside box. (You can get full openSSH server/client via Cygwin on windows)
You could also try Teredo if things are really ugly with the firewalls involved. Also lots of other tunneling methods out there. It really depends on the firewall situation.