Do any of the NetworkManager VPN plugins support IPv6? The two I've tried so far (PPTP and StrongSwan) only show an "IPv4" tab. I would have thought at least the IPsec one would support IPv6?
IPv6 over the VPNs in NetworkManager is not currently supported in 12.04 and prior releases of Ubuntu. It is a new feature introduced in a further release of NetworkManager (0.9.6.0), so it will be available, to begin with, on the OpenConnect plugin only. Such support will be available in Quantal Quetzal (Ubuntu 12.10).
There are two ways to handle IPv6 remote access.
OpenVPN and the like do an IPv4 tunnel but don't handle IPv6 which has an entirely different stack. If you have a /48 or /56 IPv6 allocation you can create a /64 network and use and 6to4 tunnel to connect over the VPN.
Use native IPv6 roaming. You will want to enable IPSec for your IPv6 network if you do this. The roaming server will need an IPv6 address where it is. It then notifies your IPv6 router where to route its traffic. This is designed to handle individual systems like laptops. At a minimum, the headers should be secured with IPv6.
As far as I know, no plugin for Network Manager supports IPv6. Even OpenVPN does not support it straightforward.
You can drop Networkmanager and use OpenVPN directly. I have put my experiences on setting up OpenVPN+IPv4+IPv6 on Serverfault: How can I setup OpenVPN with IPv4 and IPv6 using a tap device?.