Just finished fighting this for a couple of hours and thought I would write it here in case someone else has the same problem.
I have a brand new dual band airport extreme that I have setup with a tunnel to HE. The tunnel came up and I was able to ping6 ipv6.he.net fine, but was unable to connect to any HE webpages using my browser. I ended up having to change the MTU size on the laptop I was using to 1472 in order to make it work. Smaller MTU size will also work, but nothing larger.
The DSL I have uses PPPOE, so it already shrinks the usable MTU to 1492, then add the tunnel and you have 1472. I am guessing that HE has a firewall that is not allowing fragmentation, but have not looked further yet.