1. Nmap - map your network and ports with the number one port scanning tool. This tool features powerful NSE scripts that can detect vulnerabilities, misconfiguration and security related information around network services.
2. OpenVAS - open source vulnerability scanning suite manages all aspects of a security vulnerability management system from web-based dashboards.
3. OSSEC - host-based intrusion detection system or HIDS is easy to setup and configure. OSSEC has far reaching benefits for both security and operations staff.
4. Security Onion - a network security monitoring distribution that can replace expensive commercial grey boxes with blinking lights. Being easy to setup and configure the tool requires minimal effort. Start detecting your security related events on your network from brute force scanning kids to those nasty APT's.
5. Metasploit Framework – A penetration testing tool that tests all aspects of your security with an offensive focus. It also includes exploits, scanning, and auditing.