I was reviewing some Microsoft materials related to IPv6 for some presentations I am putting together and ran across some great material by Joseph Davies again that goes over some very specific reasons why it is bad to disable IPv6 on Windows Vista and Windows Server 2008 which of course also applies to Windows 7 and Server 2008R2.
In summary, you have the potential to break features in Remote Assistance, HomeGroup, DirectAccess, and Windows Mail. I would add BranchCache, Exchange Server 2007 and 2010, Microsoft Outlook and several of the tunneling methods.
I do believe there are legitimate reasons for wanting to control the IPv6 traffic that Windows 7 or Server 2008R2 is generating on your network. I would also argue that the way to do this is by having IPv6 deployed in your network so that you can have a consistent policy that matches much of what you do today for IPv4. Obviously there are different ways to deploy IPv6 but I think that a dual stack/native IPv6 deployment makes for the best solution long term. It allows the flexibility of getting to IPv6 resources and allows for a longer transition windows for IT groups to migrate all services to IPv6.
One of the surprises for many people deploying Windows Server with Exchange and using the recommended deployment practices from Microsoft is that you could have stand alone servers in a DMZ or outside your network that are NOT AD domain joined. They are in "workgroup" mode and this means that if they have a public IPv4 address they will generate a 6to4 tunnel automatically and if they are using RFC 1918 IPv4 addresses they will make use of teredo tunnels automatically. This behavior isn't desirable for most enterprises and can easily be resolved by either turning off IPv6 on those specific servers or by setting up a dual stack configuration for the server with appropriate firewall rules. Obviously you need a network firewall that can do IPv6 or rely on the Windows Firewall to do this function.
So for those that reference my earlier blog entry about turning off IPv6 tunneling - seriously consider if you really need to do that or not. You need to evaluate your scenario and determine what is right but if there is a chance you might need the OS to do one of the tunnels then doing some of the network blocking methods I mentioned might cause more work in the end.