WHM/cPanel has a lot of inbuilt services. The important configuration files and the corresponding conf file path are listed below:
The cpanel configuration file
Configuration file : cpanel.config
Path : /var/cpanel/cpanel.config
Service : cpanel
Apache – The web server
Default Port : #80
Configuration file : httpd.conf 
Path : /etc/httpd/conf/httpd.conf Or /usr/local/apache/conf/httpd.conf
Service : httpd
Exim – The mail server
Configuration file : exim.conf
Path : /etc/exim.conf
Service : exim
Bind – The name server
Default Port : 53
Configuration file : named.conf
Path : /etc/named.conf
Service : named
DB location : /var/named
FTP server
proftp
Default Port : 20, 21
Configuration file : proftpd.conf
Path : /etc/proftpd.conf
Service : proftpd
pureftp
Default Port : 20, 21
Configuration file : pure-ftpd.conf
Path : /etc/pure-ftpd.conf
Service : pure-ftpd
MySQL – DB
Default Port : 3306
Configuration file : my.cnf
Path : /etc/my.cnf
Service : mysql
PHP
Configuration file : php.ini 
Path : /usr/local/lib/php.ini (php --ini : to find conf location)
Networking Setup
/etc/sysconfig/network 
/etc/hosts - Host entries
/etc/resolv.conf - Resolver Configuration
/etc/nameserverips - Nameserver IPs
clamav – The antivirus configuration file
Configuration file : clamav.conf
Path : /etc//etc/clamav.conf
Service : clamd
Click here for Important WHM/cPanel Scripts
Other useful configuration files are;
# /var/cpanel/users/username cpanel user file
# /var/cpanel/resellers For addpkg, etc permissions for resellers.
# /var/run/chkservd  Main >> Server Status >> Service Status
# /etc/chkserv.d Main >> Service Configuration >> Service Manager
# /var/log/dcpumon  top log process
# /root/cpanel3-skel skel directory. Eg: public_ftp, public_html. (Account
Functions–>Skeleton Directory )
# /etc/wwwacct.conf account creation defaults file in WHM (Basic cPanel/WHM
Setup)
# /etc/cpupdate.conf Update Config
# /etc/ips – ip addresses on the server (except the shared ip) (IP Functions–>Show IP Address Usage )
# /etc/ipaddrpool IP Addresses which are free
# /etc/ips.dnsmaster  name server ips
# /var/cpanel/Counters To get the counter of each users.
# /var/cpanel/bandwidth To get bandwith usage of domains
# /var/cpanel/bandwidth : rrd files of domains
# /var/cpanel/username.accts : reseller accounts are listed in this files
# /var/cpanel/packages : hosting packages are listed here
# /var/cpanel/root.accts : root owned domains are listed here
# /var/cpanel/suspended : suspended accounts are listed here
# /var/cpanel/users/ : cpanel user file – theme, bwlimit, addon, parked, sub-domains all are listed in this files
# /var/cpanel/zonetemplates/ : dns zone template files are taken from here