Apache configuration file

etc/httpd/conf/httpd.conf 

Mail server configuration file

/etc/exim.conf

Name server (named)configuration file

/etc/named.conf 

Cpanel user file

/var/cpanel/users/username 

Mysql configuration file

/etc/my.cnf 

To get bandwith usage of domain

/var/cpanel/bandwidth 

Cpanel configuration file ( Tweak Settings )

/var/cpanel/cpanel.config

php configuration file ( command : php -i | grep php.ini)

/usr/local/lib/php.ini 

List of domains served by exim mail server

/etc/localdomains 

Log Files

Cpanel access log

/usr/local/cpanel/logs/access_log

Auditing log (account creations, deletions, etc)

/var/cpanel/accounting.log

Exim log file location

/var/log/exim_mainlog

Apache log file location

/var/log/apache/access.log