Disable phpMyAdmin :
chmod 000 /var/www/html/phpMyAdmin
enable:
chmod 755 /var/www/html/phpMyAdmin

Rootkits
Here’s an step by step guide to checking your server for rootkits:
http://www.howtoforge.com/scan_linux_for_rootkits

After running chkrootkit I also ran rootkit hunter by using this:
apt-get install rkhunter
rkhunter

To run a check type: rkhunter -c

There’s a server security checklist at:
http://www.cert.org/tech_tips/unix_configuration_guidelines.html

20 Linux System Monitoring Tools Every SysAdmin Should Know
http://www.cyberciti.biz/tips/top-linux-monitoring-tools.html