Google

Google : Everyone’s Favorite Search Engine
While it is far more than a security tool, Google’s massive database is a good mind for security researchers and penetration testers. You can use it to dig up information about a target company by using directives such as “site:target-domain.com” and find employee names, sensitive information that they wrongly thought was hidden, vulnerable software installations, and more. Similarly, when a bug is found in yet another popular webapp, Google can often provide a list of vulnerable servers worldwide within seconds. The master of Google hacking is Johny Long. Check out his Google Hacking Database or his excellent book: Google Hacking for Penetration Testers.

Sam Spade

Sam Spade : Freeware Windows network query tool
Sam Spade provides a consistent GUI and implementation for many handy network query tasks. It was designed with tracking down spammers in mind, but can be useful for many other network exploration, administration, and security tasks. It includes tools such as ping, nslookup, whois, dig, traceroute, finger, raw HTTP web browser, DNS zone transfer, SMTP relay check, website search, and more. Non-Windows users can enjoy online versions of many of their tools.

Perl_Python_Ruby

Perl / Python / Ruby : Portable, general-purpose scripting languages
While many canned security tools are available on this site for handling common tasks, scripting languages allow you to write your own (or modify existing ones) when you need something more custom. Quick, portable scripts can test, exploit, or even fix systems. Archives like CPAN are filled with modules such as Net::RawIP and protocol implementations to make your tasks even easier.

OpenSSH_PuTTY_SSH

OpenSSH / PuTTY / SSH : A secure way to access remote computers
SSH (Secure Shell) is the now ubiquitous program for logging into or executing commands on a remote machine. It provides secure encrypted communications between two untrusted hosts over an insecure network, replacing the hideously insecure telnet/rlogin/rsh alternatives. Most UNIX users run the open source OpenSSH server and client. Windows users often prefer the free PuTTY client, which is also available for many mobile devices. Other Windows users prefer the nice terminal-based port of OpenSSH that comes with Cygwin. Dozens of other free and proprietary clients exist. You can explore them here or here.

Ping_telnet_dig_traceroute_whois_netstat

Ping/telnet/dig/traceroute/whois/netstat : The basics
While there are many whiz-bang high-tech tools out there to assist in security auditing, don’t forget about the basics! Everyone should be very familiar with these tools as they come with most operating systems (except that Windows omits whois and uses the name tracert). They can be very handy in a pinch, although for more advanced usage you may be better off with Hping2 and Netcat.