Ok we've customized our setup a bit but not much (running trixbox 2.2.4 with freepbx 2.3.0).
When you use the phone system all day and the only time for upgrades are late at night when you are in need of sleep you end up being not at 100% some times doing a upgrade. This can cause issues with things being over written without you thinking ahead of time to save things.
So here is a list of things we've added the ampbackup.pl file to be backed up. (line 165).
/etc/zaptel.conf* /tftpboot $webroot/panel /etc/hosts /etc/resolv.conf /etc/logrotate.d/asterisk
/etc/zaptel.conf* files because we have a T1 card and analog card. They of course don't work if I switch the order as I've had to hand edit adjustments to make things work correctly from the genzaptelconf. (has to do with order of things).
/tftpboot Well we have 45 Aastra phones that boot via tftp so if the system goes away we are screwed if I have to re-create all those files again at 3am (25% of which are not in the local office but remote via VPN tunnels).
$webroot/panel since we have more then 40 phones I've had to re-adjust the panel config files and layout so I have three columns for extensions and enough space for our 26 trunks (I also have to customize 4 lines in the /var/lib/asterisk/bin/retrieve_op_conf_from_mysql.pl file to this support).
/etc/resolv.conf yea I'm just lazy I have our three name servers and 6 domains defined in it so I don't need to recreate that also.
/etc/hosts Same lazy reason as we have three servers that MUST be defined in the hosts file for our backup software to work.
If people have to have routes defined and/or special settings for the NIC you might want to backup the /etc/sysconfig/network-scripts/route-* and /etc/sysconfig/network-scripts/ifcfg-* files.
/etc/logrotate.d/asterisk I've added the "/var/log/asterisk/full" to the log rotation so it doesn't grow out of control.