Some resolvers are able to talk to nameservers using IPv6. If yours doesn't you might like this patch for BIND 8.2.3. All you need to do, is apply the patch and compile your software with the bind library rather than your native resolver. For a quick test I would suggest compiling BIND with the patch, and then try to use BIND's host tool to look up something. You must of course put the IPv6 address of a nameserver in resolv.conf. The patch is a bit ugly, but seems to work okay. It's written so that it doesn't change the external interface in any way. If your system doesn't allow sending and receiving IPv4 packets on IPv6 sockets, you cannot mix IPv4 and IPv6 addresses in resolv.conf. Thanks to Ulrich Drepper and Mark Kettenis for helpful input.
If you have problems, comments, questions or whatever, feel free to contact me.