Packet Shaper:
Nemesis: a command line packet shaper
Packit: The Packet Toolkit - A network packet shaper.
Hping by Antirez: a command line TCP/IP packet shaper
Sing: stands for ‘Send ICMP Nasty Garbage’; sends fully customizeable ICMP packets
Scapy: a new python-based packet generator

Password Cracker/Login Hacker:
John the Ripper: a well-known password cracker for Windows and *nix Systems
Djohn: a distributed password cracker based on “John the Ripper”
Cain & Abel: an advanced password recovery tool for windows systems. It sniffs the network packets an cracks authentication brute-force or with dictionary attacks.
Project RainbowCrack: Advanced instant NT password cracker
Rainbowtables: The shmoo group provides pre-generated rainbow tables for bittorrent download. The tables are generated with RainbowCrack (see above).
Windows NT password recovery tool by Peter Nordahl
THC-Dialup Login Hacker by THC. It tries to guess username and password against the modem carrier. As far as I know the only available dialup password guesser for *NIX.
Hydra by THC: a multi-protocol login hacker. Hydra is also integrated with Nessus.
Medusa: parallel network login auditor
THC imap bruter: a very fast imap password brute forcer
x25bru: a login/password bruteforcer for x25 pad
Crowbar: a generic web brute force tool (Windows only; requires .NET Framework)
MDCrack-NG: a very fast MD4/MD5/NTLMv1 hash cracker; works optionally with precomputed hash tables
Advanced Sniffers:
Wireshark (formerly known as Ethereal): an open source network protocol analyzer
Dsniff by Dug Song: a combination of very useful sniffer and man-in-the-middle attack tools
Ettercap: a multipurpose sniffer/interceptor/logger for switched LAN environments
aimsniffer: monitors AOL instant messager communication on the network
4G8: a tool ,similar to ettercap, to capture network traffic in switched environments
cdpsniffer: Cisco discovery protocol (CDP) decoding sniffer
Port Scanner / Information Gathering:
nmap: the currently most well-known port scanner. Since version 3.45 it supports version scans. Have a look at PBNJ for diffing different nmap scans.
ISECOM released their nmap wrapper NWRAP, which shows all known protocols for the discovered ports form the Open Protocol Resource Database
Nmap::Scanner: Perl output parser for nmap
Amap by THC: An advanced portscanner which determines the application behind a network port by its application handshake. Thus it detects well-known applications on non-standard ports or unknown applications on well-known ports.
vmap by THC: version mapper to determine the version (sic!) of scanned daemons
Unicornscan: a information gathering and correlation engine
DMitry (Deepmagic Information Gathering Tool): a host information gathering tool for *nix systems
Athena: a search engine query tool for passive information gathering
Security Scanner:
Nessus - In version 2 an OpenSource network scanner. Version 3 is only available in binary form and under a proprietary license.
OpenVAS: a fork of Nessus 2.2.5 (formerly known as GNessUs)
Nessj: a java based nessus (and compatibles) client (formerly known as Reason)
Paul Clip from @stake released AUSTIN, a security scanner for Palm OS 3.5+.
Webserver:
Nikto: a web server scanner with anti IDS features. Based on Rain Forest Puppies libwhisker library.
Wikto: a webserver assessment tool (Windows only; requires .NET framework)
WSDigger: a black box web pen testing tool from Foundstone (Windows based)
Metis: a java based information gathering tool for web sites
Fingerprinting:
SinFP: a fingerprinting tool which requires only an open tcp port and sends maximum 3 packets
Winfingerprint: much more than a simple fingerprinting tool.It scans for Windows shares, enumerates usernames, groups, sids and much more.
p0f 2: Michal Zalewski announced his new release of p0f 2, a passive OS fingerprinting tool. p0f 2 is a completely rewrite of the old p0f code.
xprobe2: a remote active operating system fingerprinting tool from Ofir Arkin and the xprobe2 team
Cron-OS: an active OS fingerprinting tool based on TCP timeout behavior. This project was formerly known as “RING” and is now published as a nmap addon.
Proxy Server:
Burp proxy: an interactive HTTP/S proxy server for attacking and debugging web-enabled applications
Screen-scraper: a http/https-proxy server with a scripting engine for data manipulation and searching
Paros: a man-in-the-middle proxy and application vulnerability scanner
WebScarab: a framework for analyzing web applications. One of it’s basic functionality is the usage as intercepting proxy.
War Dialers:
IWar: a classic war dialer, now also with VOIP (IAX2) support. One of a few wardialers for *nix operation systems, and the only with VOIP functionality (to my knowledge)
THC-Scan: a war dialer for DOS, Windows and DOS emulators
Malware / Exploit Collections:
packetstormsecurity.org: Huge collections of tools and exploits
ElseNot Project: The project tries to publish an exploit for each MS Security Bulltin. A script kiddie dream come true.
Offensive Computing: Another malware collection site
Securityforest: try the ExploitTree to get a collection of exploit code; have a look at the ToolTree for a huge list of pentest stuff
Databases / SQL:
sqlninja: a tool to exploit sql injection vulnerabilities in web applications with MS SQL Servers (alpha stage)
CIS Oracle Database Scoring Tool: scans Oracle 8i for compliance with the CIS Oracle Database Benchmark
SQLRecon: an active and passive scanner for MSSQL server. Works on Windows 2000, XP and 2003.
absinthe: a gui-based tool that automates the process of downloading the schema & contents of a database that is vulnerable to Blind SQL Injection (see here and here).
SQL Power Injector: a GUI based SQL injector for web pages (Windows, .Net Framework 1.1 required, Internet Explorer 5.0+ required)
Voice over IP (VOIP):
vomit (voice over misconfigured internet telephones): converts Cisco IP phone conversations into wave files
SiVuS: a VOIP vulnerability scanner - SIP protocol (beta, Windows only)
Cain & Abel: mostly a password cracker, can also record VOIP conversations (Windows only)
sipsak (SIP swis army knife): a SIP packet generator
SIPp: a SIP test tool and packet generator
Nastysip: a SIP bogus message generator
voipong: dumps G711 encoded VOIP communications to wave files. Supports: SIP, H323, Cisco Skinny Client Protocol, RTP and RTCP
Perl based tools by Thomas Skora: sip-scan, sip-kill, sip-redirectrtp, rtpproxy and ipq_rules
rtptools: a toolset for rtp recording and playing
Networkbased Tools:
yersinia: a network tool designed to take advantage of some weakeness in different network protocols (STP, CDP, DTP, DHCP, HSRP, 802.1q, VTP)
Netsed: alters content of network packets while forwarding the packets
ip6sic: a IPv6 stack integrity tester
VPN:
ike-scan: an IPSec enumeration and fingerprinting tool
ikeprobe: ike scanning tool
ipsectrace: a tool for profiling ipsec traffic in a dump file. Initial alpha release
VPNMonitor: a Java application to observer network traffic. It graphically represents network connections and highlights all VPN connections. Nice for demonstrations, if somewhat of limited use in a real pen test.
IKECrack:an IKE/IPSec cracker for pre-shared keys (in aggressive mode authentication [RFC2409])
DNSA: DNS Auditing tool by Pierre Betouin
Hunt: a session hijacking tool with curses GUI
SMAC: a Windows MAC Address Modifying Utility. Supports Windows 2000 and XP.
The WebGoat Project: a web application written in Java with intentional vulnerabilities. Supports an interactive learning environment with individual lessons.
TSCrack: a Windows Terminal Server brute forcer
Ollie Whitehouse from @stake released some new cellular phone based pentesting tools for scanning (NetScan, MobilePenTester). All tools require a Sony Ericsson P800 mobile phone. Unfortunately, @stake seems no longer to support much of their free security tools. So, use instead the alternativ download links above.
THC-FuzzyFingerprint: generates fuzzy fingerprints that look almost nearly equal to a given fingerprint/hash-sum. Very useful for MITM attacks.
BeatLM, a password finder for LM/NTLM hashes. Currently, there is no support for NTLM2 hashes. In order to get the hashes from network traffic, try ScoopLM.
THC vlogger: a linux kernel based keylogger
The Metasploit Framework: an “advanced open-source platform for developing, testing, and using exploit code”.
ATK (Attack Tool Kit): a comination of security scanner and exploit framework (Windows only)
Pirana: an exploitation framework to test the security of email content filters. See also the whitepaper
PassLoc: a tool which provides the means to locate keys within a buffer. Based on the article “Playing hide and seek with stored keys” by Adi Shamir.
Dl-Hell: identifies an executables dynamic link library (DLL) files
DHCPing: a security tool for testing dhcp security
ldapenum: a perl script for enumeration against ldap servers.
Checkpwd: a dictionary based password checker for oracle databases
NirCmd from NirSoft: a windows command line tool to manipulate the registry, initiate a dialup connection and much more
Windows Permission Identifier: a tools for auditing user permissions on a windows system
MSNPawn: a toolset for footprinting, profiling and assesment via the MSN Search. Windows-only, .NET required
snmpcheck:a tool to gather information via snmp. Works on Linux, *BSD and Windows systems.
pwdump6: extract NTLM and LanMan hashes from Windows targets