I had migrated to Tomato firmware for my home router (WRT54GL) about a year ago, so I didn't want to change firmware or buy a new router for IPv6 support.
However I found that I could log into Tomato via the SSH daemon, similar to what one would do to log into a remote Linux box. I found iptables and I added a line into iptables to allow forwarding of protocol 41 to my LAN IP that had the HE tunnel.
iptables -A wanin -p 41 -d 192.168.1.2 -j ACCEPT
That did the magic and allowed my Windows 7 desktop with the HE tunnel to work.
I did a write-up of my experience in my geeklog
P.S. I also edited /etc/iptables and added "-A wanin -p 41 -d 192.168.1.2 -j ACCEPT" hoping that my iptables change would come back after a router reboot. However, my router currently has an uptime of 306 days and I don't plan on rebooting any time soon.