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The only downside is that the tinyproxy that sits in Ubuntu 12.04 does not listen on both IPv4 and IPv6 at the same time

2013-01-04 Shame on me... I didn't test properly , but tinyproxy does work on both protocols 

I assumed that this result:

netstat -tlnpvw | grep tinyproxy
tcp6 0 0 :::8888 :::* LISTEN 3946/tinyproxy

meant that it didn't listen on v4... but I was wrong.

Listen ::
#This will accept connections on IPv6, but also on IPv4: IPv4-mapped IPv6 addresses are used:
#CONNECT Jan 04 15:29:13 [23566]: Connect (file descriptor 6): host.terena.org [::ffff:192.87.30.2]

Listen 0.0.0.0
# This will listen on IPv4 only

Listen 2001:610:148:dead::666
# This will listen only on the specified IPv6 address. Not nice, but workable.

 Hopefully this will be resolved soon...

Coda 2 drops support for IPv6

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MySQL at this moment does not support IPv6 connections, but the development versions seem to support it (sort of). There are tools to make it work, such as https://twiki.cern.ch/twiki/bin/view/EGEE/IPv6CARE.
Not A Problem Here: we have only one host running MySQL, and that will be phased out in the future any way..
Not A Problem Here: we have only one host running MySQL, and that will be phased out in the future any way.

Update 2013-03-22: We were forced to use MySQL for some stuff, but the version in Ubuntu 12.04 appears to have IPv6 support . I configured it to listen to IPv6 only:

bind-address            = '::'

apt-get

security.ubuntu.com does not work, so no security updates. Workaround: use local mirror nl.archive.ubuntu.com for security updates.

Update 2013-03-12: This has been fixed : https://lists.ubuntu.com/archives/foundations-bugs/2013-March/140037.html

Pear Net_Socket

Does not like IPv6 addresses, wrote patch.

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