These are items inside of WHM/cpanel that should be changed to secure your server.
Goto Server Setup =>> Tweak Settings
Check the following items…
Prevent users from parking/adding on common internet domains. (ie hotmail.com, aol.com)
Attempt to prevent pop3 connection floods
Default catch-all/default address behavior for new accounts – blackhole
Use jailshell as the default shell for all new accounts and modified accounts
Goto Server Setup =>> Tweak Security
Enable php open_basedir Protection
Enable mod_userdir Protection
Disabled Compilers for unprivileged users.
Goto Server Setup =>> Manage Wheel Group Users
Remove all users except for root and your main account from the wheel group.
Goto Server Setup =>> Shell Fork Bomb Protection
Enable Shell Fork Bomb/Memory Protection
When setting up Feature Limits for resellers in Reseller =>> Reseller Center, under Privileges always disable Allow Creation of Packages with Shell Access and enable Never allow creation of accounts with shell access; under Root Access disable All Features.
Goto Service Configuration =>> FTP Configuration
Disable Anonymous FTP
Goto Account Functions =>> Manage Shell Access
Disable Shell Access for all users (except yourself)
Goto Mysql =>> MySQL Root Password
Change root password for MySQL
Goto Security and run Quick Security Scan and Scan for Trojan Horses often. The following and similar items are not Trojans: