Read this post: http://codijuana.blogspot.com/2013/10/case-2-alpha-pad
Remix of the permutation ciphers' design for better security. I tried to solve the issue of frequency analysis and brute force attacks by joining padding and the alphabet matching (I called it the alpha-padding)
View a demo here: http://igenda.netau.net/codijuana/alphapadding_permutation/
Secwatch is an intrusion detection system using log analysis to detect service scan and other brute-force attempts on a server or other computer using system logs and will create temporary firewall rules to block offending IPs
using PHP (and some ShellScript) to protect your linux server against bruke force attacks(http://en.wikipedia.org/wiki/Brute_force_attack).
also keep a log in MySQL and have email reporting