Here is list of software that will make your life much easier:
Putty – A command line utility for working with your server.
cPanel / WHM Plugins
CSF or Config Server Firewall – A great addon that will help protect your server from attacks, as well as closing unused ports.
PS – if you want something added to the list, please send me an email with the link so I can check it out :
chris AT solidservers.ca