Hello,
are you referring to 6to4 and GRE tunnels ?
One of the differences is the addressing: GRE IPv4 tunnels use an IPv6 address, while 6to4 tunnels use
an IPv6 address where the prefix must embed the tunnel source IPv4 address.
The use of either ond depends on what you want to use it for, check the following document for an explanation of implementation considerations:
Information About Implementing Tunneling for IPv6
http://www.cisco.com/univercd/cc/td/doc/product/software/ios123/123cgcr/ipv6_c/sa_tunv6.htm#wp1027177
HTH,
GP