Source: http://g33kinfo.com/info/archives/584

This script will copy everything necessary for a full cpanel -> cpanel transfer.
You need to open the script up and change 127.0.0.1 to the FQDN or IP of the
target server. It will first create a key pair and then transfer it to the
target server. Root level access is required for this script to work properly.
After this runs you will need to update the network configuration on the new
server and reboot or restart networking.

Code:
#!/bin/sh
#
# HOST = User + IP / Hostname to copy files TO.
HOST="root@PUTDESTINATIONIP"

echo Creating key pair...
ssh-keygen -t dsa
echo Create .ssh directory on destination server...
ssh $HOST 'mkdir /root/.ssh'
scp /root/.ssh/id_dsa.pub $HOST:~/.ssh/authorized_keys

# /etc User / IP's + passwd files
echo Transferring /etc
rsync -aqHl -e ssh /etc/passwd $HOST:/root/
rsync -aqHl -e ssh /etc/shadow $HOST:/root/
rsync -aqHl -e ssh /etc/group $HOST:/root/
rsync -aqHl -e ssh /etc/wwwacct.conf $HOST:/etc/
rsync -aqHl -e ssh /etc/quota.conf $HOST:/etc/
rsync -aqHl -e ssh /etc/domainalias $HOST:/etc/
rsync -aqHl -e ssh /etc/remotedomains $HOST:/etc/
rsync -aqHl -e ssh /etc/localdomains $HOST:/etc/
rsync -aqHl -e ssh /etc/userdomains $HOST:/etc/
rsync -aqHl -e ssh /etc/valiases $HOST:/etc/
rsync -aqHl -e ssh /etc/vfilters $HOST:/etc/
rsync -aqHl -e ssh /etc/vmail $HOST:/etc/
rsync -aqHl -e ssh /etc/trueuserdomains $HOST:/etc/
rsync -aqHl -e ssh /etc/trueuserowners $HOST:/etc/
rsync -aqHl -e ssh /etc/ips $HOST:/etc/
rsync -aqHl -e ssh /etc/ipaddresspool $HOST:/etc/
rsync -aqHl -e ssh /etc/services $HOST:/etc/

# ftpd files
echo Transferring FTP configs
rsync -aqHl -e ssh /etc/sysconfig/pure-ftpd $HOST:/etc/sysconfig/
rsync -aqHl -e ssh /etc/pure-ftpd.conf $HOST:/etc/
rsync -aqHl -e ssh /etc/pure-ftpd $HOST:/etc/
rsync -aqHl -e ssh /etc/proftpd $HOST:/etc/
rsync -aqHl -e ssh /etc/proftpd.* $HOST:/etc/

# /var
echo Transferring /var
rsync -aqHl -e ssh /var/cpanel $HOST:/var/
rsync -aqHl -e ssh /var/spool/cron $HOST:/var/spool/

# /usr config - 3rdparty
echo Transferring 3rd party and SSL certs
rsync -aqHl -e ssh /usr/share/ssl $HOST:/usr/share/
rsync -aqHl -e ssh/usr/local/cpanel/3rdparty/mailman $HOST:/usr/local/cpanel/3rdparty/
rsync -aqHl -e ssh /usr/local/cpanel/base/frontend $HOST/usr/local/cpanel/base/

# Apache
echo Transferring Apache configs
rsync -aqHl -e ssh /usr/local/apache/conf $HOST:/usr/local/apache/
rsync -aqHl -e ssh /usr/local/apache/libexec $HOST:/usr/local/apache/
rsync -aqHl -e ssh /usr/local/frontpage $HOST:/usr/local/

# Mysql config
echo Transferring MySQL configs
rsync -aqHl -e ssh /root/.my.cnf $HOST:/root/
rsync -aqHl -e ssh /etc/my.cnf $HOST:/etc/

# Named
echo Transferring zone files and bind configs
rsync -aqHl -e ssh /var/named $HOST:/var/
rsync -aqHl -e ssh /etc/named.conf $HOST:/etc/
rsync -aqHl -e ssh /etc/rndc.conf $HOST:/etc/

#User Files
# Mysql
echo Transferring MySQL databases
rsync -aqHl -e ssh /var/lib/mysql/* $HOST:/var/lib/mysql/

# Home
echo Tansferring /home
rsync -aqHl -e ssh /home/* $HOST:/home/
PS: cloning MySQL using rsync is not recommended because of possible InnoDB corruption (source), mysqldump is advised. Anyone have idea on other commands to sync cpanel files and MySQLs between servers?