I've noticed the topic of configuring iptables or other firewall with IPv6 comes up once in a while on this forum. I think Firewall Builder can help. It is an OSS interactive firewall configuration and management tool. We have started beta testing of the new version (Firewall Builder 3.0) which provides support for ipv6 with iptables, PF and Cisco IOS extended access lists. I thought this might be of interest for readers here. More information is available on the web site:
http://www.fwbuilder.org/docs/firewall_builder_3_features.html