At the time of this writing, IPv6 support in guests requires you to apply an additional patch on top of the Linux-VServer patch. The IPv6 patch can be fetched from the official source: Bruno Prémont's IPv6 patches, and sometimes rediffs against later kernels are available from my patch directory.
To use the patch, you need util-vserver 0.30.212 or newer. These versions support IPv6 natively, so you just need to put the address in
/etc/vservers/<guest>/interfaces/X/ip and start the guest to get it an IPv6 address.
Starting with linux-vserver-2.3 IPv6 support is included in the main source code. No need to apply any extra patches. You will need to have util-vserver 0.30.214 or newer if you are using the 2.3+ patches. There is no need to add the prefix into