I would dearly love to be able to run an IPv6 network at home for experimental purposes, but there are some applications which are not IPv6 aware yet. I'll list them here and as support is added I can cross them off.
<h3>Supported</h3>
Linux core OS
Windows core OS
Bind
Dovecot
OpenSSH
Apache
Thunderbird
Firefox
DHCPv6
vsftpd
ntpd
Spamassassin
SecureCRT (requires upgrade to v5)
Cisco IOS Router will also require a software upgrade to Advanced IP Services (but at least it's an option).
MySQL
<h3>Does not yet support IPv6</h3>
Squid
<h3>Unknown</h3
MSN Messenger - believed to be OK
Amavis
Samba