Insecure.org has a list of the 75 top tools. The top 5 are:
Nessus is a remote security scanner for Linux, BSD, Solaris, and other Unices. It is plug-in-based, has a GTK interface, and performs over 1200 remote security checks. It allows for reports to be generated in HTML, XML, LaTeX, and ASCII text, and suggests solutions for security problems.
Ethereal is a free 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, viewing summary and detail information for each packet. Ethereal has several powerful features, including a rich display filter language and the ability to view the reconstructed stream of a TCP session. A text-based version called tethereal is included.
Snort is a lightweight network intrusion detection system, capable of performing real-time traffic analysis and packet logging on IP networks. It can perform protocol analysis, content searching/matching and can be used to detect a variety of attacks and probes, such as buffer overflows, stealth port scans, CGI attacks, SMB probes, OS fingerprinting attempts, and much more. Snort uses a flexible rule based language to describe traffic that it should collect or pass, and a modular detection engine. Many people also suggested that the Analysis Console for Intrusion Databases (ACID) be used with Snort.