Use secure passwords (change them often) and keep all software on your server up to date, including PHP and scripts.
Don't install things there that you won't use.
By the way, you're not using Linux? Then what are you using? cPanel isn't available for Windows yet (I think it's coming out in beta soon, though). You're obviously using some flavor of Unix, and it's probably Linux (CentOS, maybe?)
1. Use mod_security
2. Use mod_evasive
3. Use iptables for intruders
4. I like Logwatch
I think there will be a nice article in WMT's article section in a few weeks about additional security measures that can be taken. 
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