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There is a good blog on deploying IPv6 by the authors of O'Reilly's book on IPv6 Network Administration. Following this you get a good sense of the kinds of corner cases that you will need to deal with.

For an effective and successful IPv6 transition it is important to collect and track metrics measuring: The impact of IPv6 on IPv4, The user experience for IPv6 enabled services compared to the user experience for the existing IPv4 enabled services. Baselining the existing environment and services and then monitoring both IPv4 and IPv6 throughout IPv6 enablement will avoid the default finger pointing and will provide the metrics needed in reporting on the progress and success of the project.

In addition to planning the IPv6 transport network deployment, you also need to consider DNS and Naming Issues carefully. DNS servers will send AAAA records to hosts which may have IPv6 capability on the host, but not on their access network. For many years, Apple Macs, Linux Machines and Solaris servers have supported IPv6 out of the box. If they try to use the IPv6 addresses that you advertise, but their access network does not support IPv6, your site will appear to be malfunctioning.