MySQL at this moment does not support IPv6 connections, but the development versions seem to support it (sort of). There are tools to make it work, such as https://twiki.cern.ch/twiki/bin/view/EGEE/IPv6CARE.
Not A Problem Here: we have only one host running MySQL, and that will be phased out in the future any way.
Update 2013-03-22: We were forced to use MySQL for some stuff, but the version in Ubuntu 12.04 appears to have IPv6 support . I configured it to listen to IPv6 only:
bind-address = '::'
security.ubuntu.com does not work, so no security updates. Workaround: use local mirror
nl.archive.ubuntu.com for security updates.