Samba 3 configuration files should support IPv6 address formats and interfaces. Specifically:
1) Config files should support IPv6 address formats as per RFC4291 in every place that an IPv4 address can be used. Also see http://www.iana.org/assignments/ipv6-address-space for details of allocated prefixes.
2) Samba should treat any IPv4 addresses with prefixes of ::ffff:0:0/96 as duplicates of the IPv4 address found in the least significant 32 bits.
Please let me know if you need any help with this or testing. I'd be glad to answer any questions.
Samba 3 has ipv6 support for a long time now