Google has confirmed they are working on upgrading Google Webmaster Tools to support IPv6 Web sites.
Google Product Manager, Christina S. Chen, said in a Google Webmaster Help thread that Google is working on making the webmaster toolset work for IPv6 web sites.
A Webmaster complained that his IPv6 only web site can't be added to Google Webmaster Tools and Christina replied:
Unfortunately, we do not yet support IPv6 only websites, but we're working on doing so.
Most SEOs and Webmasters are not concerned with getting their IPv6 Websites indexed by Google. Rather, Webmasters are concerned that their IPv4 Websites will not be supported in the future. For more on that topic, see our post named IPv6 Coming: SEOs May Want To Prepare.
The site in question here is http://ipv6.mizoch.eu/ and honestly, I cannot even get to it, so I assume my ISP won't resolve to IPv6 websites or the site itself is down at the moment.
Google did not give an ETA for when they will support IPv6 websites within Google Webmaster Tools, but I suspect it might coincide with IPv6 World Day in June.
Forum discussion at Google Webmaster Help.