Wow, this is cool: the Remote Desktop Viewer (VNC) in Ubuntu 9.04 Jaunty works over IPv6. I'm testing this on Jaunty Alpha 6 and it just works: type in the IPv6 address like [2001::1:2:3] or the full name, and connect. You can also use "vinagre <ipv6 name or address" from the command line.
BTW: a desktop that's viewable, is also announce via Avahi / Zeroconf / Rendezvous. That's handy on LANs.
PS: You can make your own Ubuntu desktop viewable via System -> Preferences -> Remote Desktop.