@Chaz As far as I can see, to make Anope capable of connecting via IPv6 youd only need to modify src/sockutil.c (in the conn() function) (perhaps to use getaddrinfo() instead of gethostbyname(), much like Denora currently does (accidentally found that Denora can connect via IPv6) In theory the conn() function from Denora, with maybe minor changes should be compatible with Anope's conn() function, at least the prototypes are the same.
As for other internal recognition of IPv6 IP's in IRCd protocol messages, that's another task entirely.