1. Nmap ("Network Mapper")
Nmap is a free and open source (license) utility for network exploration or security auditing. Many systems and network administrators also find it useful for tasks such as network inventory, managing service upgrade schedules, and monitoring host or service uptime. Nmap uses raw IP packets in novel ways to determine what hosts are available on the network, what services (application name and version) those hosts are offering, what operating systems (and OS versions) they are running, what type of packet filters/firewalls are in use, and dozens of other characteristics. It was designed to rapidly scan large networks, but works fine against single hosts. Nmap runs on all major computer operating systems, and both console and graphical versions are available.
2. John the Ripper
John the Ripper is a free password cracking software tool initially developed for the UNIX operating system. It is one of the most popular password testing/breaking programs as it combines a number of password crackers into one package, autodetects password hash types, and includes a customizable cracker. It can be run against various encrypted password formats including several crypt password hash types most commonly found on various Unix flavors (based on DES, MD5, or Blowfish), Kerberos AFS, and Windows NT/2000/XP/2003 LM hash. Additional modules have extended its ability to include MD4-based password hashes and passwords stored in LDAP, MySQL and others.
3. Nessus
Nessus is a comprehensive vulnerability scanning software. Its goal is to detect potential vulnerabilities on the tested systems such as:
-Vulnerabilities that allow a remote cracker to control or access sensitive data on a system.
-Misconfiguration (e.g. open mail relay, missing patches, etc).
-Default passwords, a few common passwords, and blank/absent passwords on some system accounts. Nessus can also call Hydra (an external tool) to launch a dictionary attack.
-Denials of service against the TCP/IP stack by using mangled packets
Nessus is the world's most popular vulnerability scanner, estimated to be used by over 75,000 organizations worldwide. It took first place in the 2000, 2003, and 2006security tools survey from SecTools.Org.
4. Aircrack - The fastest available WEP/WPA cracking tool
Aircrack is a suite of tools for 802.11a/b/g WEP and WPA cracking. It can recover a 40 through 512-bit WEP key once enough encrypted packets have been gathered. It can also attack WPA 1 or 2 networks using advanced cryptographic methods or by brute force. The suite includes airodump (an 802.11 packet capture program), aireplay (an 802.11 packet injection program), aircrack (static WEP and WPA-PSK cracking), and airdecap (decrypts WEP/WPA capture files).
5. Nikto
Nikto is an Open Source (GPL) web server scanner which performs comprehensive tests against web servers for multiple items, including over 3200 potentially dangerous files/CGIs, versions on over 625 servers, and version specific problems on over 230 servers. Scan items and plugins are frequently updated and can be automatically updated (if desired).
Nikto is a good CGI scanner, there are some other tools that go well with Nikto (focus on http fingerprinting or Google hacking/info gathering etc, another article for just those).
6. Snort - Everyone's favorite open source IDS
This lightweight network intrusion detection and prevention system excels at traffic analysis and packet logging on IP networks. Through protocol analysis, content searching, and various pre-processors, Snort detects thousands of worms, vulnerability exploit attempts, port scans, and other suspicious behavior. Snort uses a flexible rule-based language to describe traffic that it should collect or pass, and a modular detection engine. Also check out the free Basic Analysis and Security Engine (BASE), a web interface for analyzing Snort alerts.
7. WireShark
Wireshark (known as Ethereal until a trademark dispute in Summer 2006) is a fantastic open source network protocol analyzer for Unix and Windows. It allows you to examine data from a live network or from a capture file on disk. You can interactively browse the capture data, delving down into just the level of packet detail you need. Wireshark has several powerful features, including a rich display filter language and the ability to view the reconstructed stream of a TCP session. It also supports hundreds of protocols and media types. A tcpdump-like console version named tethereal is included. One word of caution is that Ethereal has suffered from dozens of remotely exploitable security holes, so stay up-to-date and be wary of running it on untrusted or hostile networks (such as security conferences).
8. Chkrootkit
Chkrootkit (Check Rootkit) is a common Unix-based program intended to help system administrators check their system for known rootkits. It is a shell script using common UNIX/Linux tools like the strings and grep commands to search core system programs for signatures and for comparing a traversal of the /proc filesystem with the output of the ps (process status) command to look for discrepancies.
It can be used from a "rescue disc" (typically a Live CD) or it can optionally use an alternative directory from which to run all of its own commands. These techniques allow chkrootkit to trust the commands upon which it depend a bit more.
There are inherent limitations to the reliability of any program that attempts to detect compromises (such as rootkits and computer viruses). Newer rootkits may specifically attempt to detect and compromise copies of the chkrootkit programs or take other measures to evade detection by them.
9. Kismet
Kismet is an console (ncurses) based 802.11 layer2 wireless network detector, sniffer, and intrusion detection system. It identifies networks by passively sniffing (as opposed to more active tools such as NetStumbler), and can even decloak hidden (non-beaconing) networks if they are in use. It can automatically detect network IP blocks by sniffing TCP, UDP, ARP, and DHCP packets, log traffic in Wireshark/TCPDump compatible format, and even plot detected networks and estimated ranges on downloaded maps. As you might expect, this tool is commonly used for wardriving. Oh, and also warwalking, warflying, and warskating.
10. Hping
Hping is a free packet generator and analyzer for the TCP/IP protocol. Hping is one of the de facto tools for security auditing and testing of firewalls and networks, and was used to exploit the idle scan scanning technique (also invented by the hping author), and now implemented in the NmapSecurity Scanner. The new version of hping, hping3, is scriptable using the Tcl language and implements an engine for string based, human readable description of TCP/IP packets, so that the programmer can write scripts related to low level TCP/IP packet manipulation and analysis in very short time.
Like most tools used in computer security, hping is useful to both system administrators and crackers (or script kiddies).
11. Metasploit Framework
Metasploit took the security world by storm when it was released in 2004. No other new tool even broke into the top 15 of this list, yet Metasploit comes in at #5, ahead of many well-loved tools that have been developed for more than a decade. It is an advanced open-source platform for developing, testing, and using exploit code. The extensible model through which payloads, encoders, no-op generators, and exploits can be integrated has made it possible to use the Metasploit Framework as an outlet for cutting-edge exploitation research. It ships with hundreds of exploits, as you can see in their online exploit building demo. This makes writing your own exploits easier, and it certainly beats scouring the darkest corners of the Internet for illicit shellcode of dubious quality. Similar professional exploitation tools, such as Core Impact and Canvas already existed for wealthy users on all sides of the ethical spectrum. Metasploit simply brought this capability to the masses.
12. Netcat
Netcat is a computer networking utility for reading from and writing to network connections on either TCP or UDP.
Netcat was voted the second most useful network security tool in a 2000 poll conducted by insecure.org on the nmap users mailing list. In 2003, it gained fourth place, a position it also held in the 2006 poll.
The original version of netcat is a UNIX program. Its author is known as *Hobbit*. He released version 1.1 in March of 1996.
Netcat is fully POSIX compatible and there exist several implementations, including a rewrite from scratch known as GNU netcat.
13. THC Hydra
When you need to brute force crack a remote authentication service, Hydra is often the tool of choice. It can perform rapid dictionary attacks against more then 30 protocols, including telnet, ftp, http, https, smb, several databases, and much more. Like THC Amap this release is from the fine folks at THC.
14. Tcpdump
Tcpdump is a common computer network debugging tool that runs under the command line. It allows the user to intercept and display TCP/IP and other packets being transmitted or received over a network to which the computer is attached.
In some Unix-like operating systems, a user must have superuser privileges to use tcpdump because the packet capturing mechanisms on those systems require elevated privileges. However, the -Z option may be used to drop privileges to a specific unprivileged user after capturing has been set up. In other Unix-like operating systems, the packet capturing mechanism can be configured to allow non-privileged users to use it; if that is done, superuser privileges are not required.
The user may optionally apply a BPF-based filter to limit the number of packets seen by tcpdump; this renders the output more usable on networks with a high volume of traffic.
15. Ettercap
In case you still thought switched LANs provide much extra security
Ettercap is a terminal-based network sniffer/interceptor/logger for ethernet LANs. It supports active and passive dissection of many protocols (even ciphered ones, like ssh and https). Data injection in an established connection and filtering on the fly is also possible, keeping the connection synchronized. Many sniffing modes were implemented to give you a powerful and complete sniffing suite. Plugins are supported. It has the ability to check whether you are in a switched LAN or not, and to use OS fingerprints (active or passive) to let you know the geometry of the LAN.
16. OpenSSH 
OpenSSH is a Free and Open Source version of the SSH connectivity tools providing encrypted communication sessions over a computer network. It encrypts all traffic (including passwords) to effectively eliminate eavesdropping, connection hijacking, and other attacks. Additionally, OpenSSH provides secure tunneling capabilities and several authentication methods, and supports all SSH protocol versions.
17. Tripwire 
Tripwire is a security and data integrity tool that is useful for monitoring and alerting on specific file change(s) on a range of systems. Used with system files on a regular basis, Tripwire can notify system administrators of corrupted or tampered files, so damage control measures can be taken in a timely manner.
18. Dsniff
Dsniff is suite of powerful network auditing and penetration-testing tools and utilities that includes code to parse many different application protocols and extract interesting information. The information that can be obtained from this sniff application are: usernames and passwords, web pages being visited, contents of email, etc.
19. RainbowCrack
RainbowCrack is a password hash cracker that makes use of a large-scale time-memory trade-off. It differs from "conventional" brute force crackers in that it uses large pre-computed tables called rainbow tables to reduce the length of time needed to crack a password drastically.
20. Rkhunter
Rkhunter scans for rootkits, backdoors and possible local exploits. It does this by comparing SHA-1 hashes of important files with known good ones in online database, searching for default directories (of rootkits), wrong permissions, hidden files, suspicious strings in kernel modules, and special testsfor Linux and FreeBSD.
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