Backbone design

keep in mind - "simple, robust and scalable"
IPv4/v6 dual stack routers
IOS 12.2T images, all recent JunOS, Hitachi, NEC, Fujitsu...
PC router with *BSD can easily handle traffic of today - IPv4:IPv6 traffic = 800:1 (measured at Tokyo IX last year)

Routing
BGP4+ over IPv6 for IBGP/EBGP
RIPng
(OSPFv3 - vendor support is still poor)
RFC2772-based route filters at EBGP routers
Links
RFC2893 configured tunnels (within your AS only)
IPv6 PPP on leased lines
IPv6 over ethernet/ATM/what-have-you