Some of the most common things I do and others I cannot inform here but can send you detailed note after performing the hardening
Firewall Installation/Configuration
Login Failure Daemon
Linux Socket Monitor
Remove unused processes
Install Logwatch
OpenSSH configuration check
Rootkit Hunter
Chkrootkit
Full OS Patching/Updating
Name server configuration check
Apache tune and check
MySQL tune and check
Secure /tmp /var/tmp /dev/shm
Delete unnecessary OS users
Remove SUID/GUID from binaries
mod_security
PHP hardening