ping6 he.net does not work (and some other HE hosts in 2001::/16 are not accesible), but another hosts (not in 2001::/16 network) are accesible.
# ping6 he.net
PING he.net(he.net) 56 data bytes
^C
--- he.net ping statistics ---
16 packets transmitted, 0 received, 100% packet loss, time 15004ms
# traceroute -6 he.net
traceroute to he.net (2001:470:0:76::2), 30 hops max, 80 byte packets
1 * * *
2 * * *
3 * * *
4 * * *
5 * * *
6 * * *
7 * * *
8 * * *
9 * * *
10 * * *
11 * * *
12 * * *
13 * * *
14 * * *
15 * * *
16 * * *
17 * * *
18 * * *
19 * * *
20 * * *
21 * * *
22 * * *
23 * * *
24 * * *
25 * * *
26 * * *
27 * * *
28 * * *
29 * * *
30 * * *
# ping6 ipv6.google.com
PING ipv6.google.com(lpp01m01-in-x67.1e100.net) 56 data bytes
64 bytes from lpp01m01-in-x67.1e100.net: icmp_seq=1 ttl=53 time=118 ms
64 bytes from lpp01m01-in-x67.1e100.net: icmp_seq=2 ttl=53 time=118 ms
64 bytes from lpp01m01-in-x67.1e100.net: icmp_seq=3 ttl=53 time=118 ms
64 bytes from lpp01m01-in-x67.1e100.net: icmp_seq=4 ttl=53 time=118 ms
^C
--- ipv6.google.com ping statistics ---
4 packets transmitted, 4 received, 0% packet loss, time 3004ms
rtt min/avg/max/mdev = 118.259/118.722/118.964/0.444 ms
# traceroute -6 ipv6.google.com
traceroute to ipv6.google.com (2a00:1450:4010:c00::67), 30 hops max, 80 byte packets
1 * * *
2 * * *
3 * * *
4 * * *
5 2001:4860::1:0:11 (2001:4860::1:0:11) 90.361 ms 2001:4860::1:0:10 (2001:4860::1:0:10) 89.837 ms 2001:4860::1:0:11 (2001:4860::1:0:11) 90.327 ms
6 2001:4860::8:0:3015 (2001:4860::8:0:3015) 83.453 ms 83.568 ms 84.047 ms
7 2001:4860::8:0:2e9b (2001:4860::8:0:2e9b) 91.855 ms 91.789 ms 92.981 ms
8 2001:4860::8:0:3098 (2001:4860::8:0:3098) 98.624 ms 98.686 ms 98.672 ms
9 2001:4860::8:0:26e6 (2001:4860::8:0:26e6) 118.748 ms 119.485 ms 119.679 ms
10 2001:4860::2:0:2aaf (2001:4860::2:0:2aaf) 119.049 ms 141.893 ms 118.380 ms
11 2001:4860:0:1::466 (2001:4860:0:1::466) 119.392 ms 118.855 ms 130.236 ms
12 lpp01m01-in-x67.1e100.net (2a00:1450:4010:c00::67) 119.573 ms 119.502 ms 119.897 ms
# ip tunnel show
sit0: ipv6/ip remote any local any ttl 64 nopmtudisc 6rd-prefix 2002::/16
tun_ipv6: ipv6/ip remote 216.66.80.90 local 84.204.173.30 dev eth2 ttl 255 6rd-prefix 2002::/16
# route -6
Kernel IPv6 routing table
Destination Next Hop Flag Met Ref Use If
2001:470:27:56::/64 :: Un 256 0 0 tun_ipv6
2001:470:28:56::/64 :: U 256 0 0 eth1
fe80::/64 :: U 256 0 0 eth0
fe80::/64 :: U 256 0 0 eth1
fe80::/64 :: U 256 0 0 eth2
fe80::/64 :: Un 256 0 0 tun_ipv6
::/0 :: U 1006 0 0 tun_ipv6
::/0 :: !n -1 1 1986 lo
::1/128 :: Un 0 2 149 lo
2001:470:27:56::/128 :: Un 0 1 0 lo
2001:470:27:56::2/128 :: Un 0 1 198 lo
2001:470:28:56::/128 :: Un 0 1 0 lo
2001:470:28:56::1/128 :: Un 0 1 19 lo
fe80::/128 :: Un 0 1 0 lo
fe80::/128 :: Un 0 1 0 lo
fe80::/128 :: Un 0 1 0 lo
fe80::54cc:ad1e/128 :: Un 0 1 0 lo
fe80::205:5dff:fe74:85f9/128 :: Un 0 1 40 lo
fe80::20f:eaff:feb1:a7b4/128 :: Un 0 1 0 lo
fe80::211:95ff:feed:9b3/128 :: Un 0 1 0 lo
ff00::/8 :: U 256 0 0 eth0
ff00::/8 :: U 256 0 0 eth1
ff00::/8 :: U 256 0 0 eth2
ff00::/8 :: U 256 0 0 tun_ipv6
::/0 :: !n -1 1 1986 lo
That's strange.... no problems here
[carl@mars ~]$ ping6 he.net
PING6(56=40+8+8 bytes) 2001:470:c27d:e000:20c:29ff:fefa:4de7 --> 2001:470:0:76::2
16 bytes from 2001:470:0:76::2, icmp_seq=0 hlim=58 time=71.639 ms
16 bytes from 2001:470:0:76::2, icmp_seq=1 hlim=58 time=71.393 ms
16 bytes from 2001:470:0:76::2, icmp_seq=2 hlim=58 time=71.602 ms
16 bytes from 2001:470:0:76::2, icmp_seq=3 hlim=58 time=71.478 ms
16 bytes from 2001:470:0:76::2, icmp_seq=4 hlim=58 time=71.655 ms
^C
--- he.net ping6 statistics ---
5 packets transmitted, 5 packets received, 0.0% packet loss
round-trip min/avg/max/std-dev = 71.393/71.553/71.655/0.101 ms
I am using the same tunnel server, and I don't see the problem. If I traceroute to your IPs 2001:470:28:56::1 and 2001:470:27:56::2 I get a response from the tunnel server, but not from your system. So it looks like the problem is with the tunnel between your router and the tunnel server.
A tcpdump of the 6in4 traffic would be helpful. Could you run a tcpdump on the traffic between your router and the Internet?