What we are using on IPv6 (1):

Today's typical Internet applications
www, mail, FTP, SSH, ...

Network operation tools
DNS, ping, traceroute, firewall

Routing protocols
RIPng, OSPFv3, BGP-4+, (PIM-DM), PIM-SM

IPsec
for end-to-end communication (e.g. POP with IPsec)
mainly in transport mode