Protection

Cyber Security and Information Infrastructure Protection
Practical measures for critical infrastructure protection, intrusion prevention and threat assessment.
http://www.citi.umich.edu/u/provos/cybersecurity/

Deception Toolkit
Make your system seem to have network security bugs, and log attack attempts.
http://all.net/contents/dtk.html

FakeBo
Fakes trojan servers (Back Orifice, NetBus) and logs every attempt from client.
http://cvs.linux.hr/fakebo/

Flawfinder
Examines source code looking for security weaknesses.
http://www.dwheeler.com/flawfinder/

Guarded Memory Move (GMM)
The GMM library can be used to prevent and study buffer overflows exploits
http://www.xmailserver.org/gmm.html

Libsafe
Free software (GNU license) from Bell Labs for protecting internet servers from buffer overflow attacks, one of the most commonly exploited security vulnerabilities.
http://www.research.avayalabs.com/gcm/usa/en-us/initiatives/all/nsr.htm&Filter=ProjectTitle:Libsafe&Wrapper=LabsProjectDetails&View=LabsProjectDetails

Samhain
A tool for file integrity checking that optionally can be used as a client/server application for centralized monitoring of networked hosts.
http://la-samhna.de/samhain/

TCP Wrappers and other security tools
This is the main FTP site for security tools and papers from Wietse Venema.
ftp://ftp.porcupine.org/pub/security/index.html

Tripwire Security Systems, Inc.
Tripwire, file integrity assessment tool for UNIX.
http://www.tripwiresecurity.com/