I've been using IPv6 for approximately 4 years now and about 50% of my traffic goes over the tunnel courtesy of Hurricane Electric.
One of my token annoyances since going all Mac is the IPv6 setting didn't seem to stick across reboots or sleep cycles. I seem to have found the solution, courtesy of this blog post
networksetup -setv6automatic Wi-Fi
networksetup -setv6automatic Ethernet
For a MacBook with a Thunderbolt Adapter:
networksetup -setv6automatic "Thunderbolt Ethernet"
To go back to disabling it, change -setv6automatic to -setv6off.