For about a month or so Squid v3.1 is now in experimental ready to use and ready for getting tested by a wider community base. So I installed it by changing my sources.lists deb-src line to experimental instead of unstable, apt-get update, apt-get build-dep squid3 and apt-get -b source squid3. Compilation went fine and flawlessly on unstable. On stable/lenny you'll need to install squid-langpack as well from unstable.
After installing the resulting *.deb files, there was no need to change or update the configuration for squid3: if a request/domain lookup results in an IPv6 address, squid3 will use it and gives precedence over the IPv4 address. If there's no IPv6 address for that requested domain, nothing changes from the old behaviour. So, when a page is requested by an IPv4 client, squid3 will contact the site via the IPv6 address if possible and deliver the page to the client via IPv4. This is the same (and naturally expected) behavior as in polipo, another IPv4/IPv6 capable proxy. Polipo is a small proxy with less functionality than squid3, but it has some issues from time to time that needs a restart of its service. Additionally I would prefer just one proxy running on my system. So, now I'm able to just use squid3 for all of my proxy tasks again.
Using a IPv4/IPv6 capable proxy is by the way a good method to increase IPv6 visibility, especially when you fear the (amazing small) workload to deploy IPv6 in your own network.