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After a Windows 2008 server is newly provisioned, by default both IIS 6.0 and 7.0 are installed.

Version 7.0 is where you will want to establish and use IPv6. FTP is defaulted to IIS 6.0 and will need to be uninstalled and FTP for IIS 7.0 will need to be downloaded and installed if the use is needed to support IPv6. 

Links:

32bit OS = http://www.iis.net/downloads/default.aspx?tabid=34&g=6&i=1619

64bit OS = http://www.iis.net/downloads/default.aspx?tabid=34&g=6&i=1620

IPv6 Bindings

IP Binding specifies from which IP addresses the System Management Homepage accepts requests from and provides control over which nets and subnets requests are processed. Administrators can configure the System Management Homepage to only bind to addresses specified in the IP Binding page. A maximum of five subnet IP addresses and Netmasks can be defined. An IP address on the server is bound if it matches one of the entered IP Binding addresses after the mask is applied.

NOTE:  The System Management Homepage always binds to 127.0.0.1. If IP Binding is enabled and no subnet/mask pairs are configured, then the System Management Homepage is only available to 127.0.0.1. If IP Binding is not enabled, you bind to all addresses.

(Definition from: http://h30097.www3.hp.com/cma/docs/eng/tru64unx/t64_715.htm)

In the IIS manager, Drilling down to the website on the left hand pane and selecting the site will bring up the Web Site Home (example of Default Web Site Home)

 The right hand Pane of this window houses the Action menu and where you can edit site bindings. Selecting bindings will give you the Site bindings defaulted with a ‘*’ and no IP addresses. You can from here manually enter IPv6 addresses and IIS will check the validity of the address (see Pictures below). If you are selecting an IPv6 address from the drop down, please be aware that if your server is in a domain, the Domain Controller could be assigning a temp IPv6 address and this will break the binding every time the temp address changes.

Domain Restrictions are supported for IPv6 but the entries must be made manually in the \inetpub\History\CFGHITSTORY_0000000002\applicationHost.config file. This file should be backed up before any changes are made in case it needs to be restored.