I install some of the following software to help me debug and make it more secure.
sudo apt-get install fail2ban bwm-ng htop iotop iftop nethogs tcptrack
fail2ban - blocks failed logins for a number of services (a must for me) bwm-ng - bandwidth monitor (generally good to see the traffic on a server) htop - updated top command to see CPU/RAM/processes running (just nicer) iotop - see disk usage and the process (handy for checking problems) iftop - connections and their traffic in/out (can toggle hostnames and ports etc) nethogs - another network software to see traffic and process/user/IP tcptrack - ability to quickly see SYN floods or unwanted traffic