What I won't discuss

User security issue
$IFS hacks, $PATH problems, password/account sharing, authentication methods (shadow, one time passwords, LDAP, SSH keys, PAM, kerberos, biometrics, two factor authentication, etc)

Common user programming mistakes
strcpy, strcat, gets, sprintf, vsprintf, trusting user input, using csh

User-space security issues
buffer overflows, format string attacks, viruses, trojans, TCP Wrappers, restricted shells, LD_PRELOAD

Administration/configuration issues
Running unnecessary services, poor file permissions,

Audit / Log analysis /  Scanning tools
Tripwire, AIDE, Tiger, SATAN's offspring, NSAT, swatch, Nessus, etc.