Lynis is an auditing and hardening tool for Unix derivatives like Linux/BSD/Solaris. It scans systems to detect software and security issues. Besides security-related information, it will also scan for general system information, installed packages, and possible configuration mistakes. The software is aimed at assisting automated auditing, software patch management, and vulnerability and malware scanning of Unix-based systems.
Xplico is an IP traffic decoder that extracts data from an Internet traffic capture. From a pcap file, it can extracts each email (POP, IMAP, and SMTP protocols), all HTTP content, VoIP calls (SIP, RTP, H323, MEGACO, MGCP), IRC, MSN, and so on. It isn't a packet sniffer or a network protocol analyzer, but rather an IP/Internet traffic decoder or network forensic analysis tool (NFAT).
Yet Another Flowmeter (YAF) is a tool for network flow capture, primarily designed to operate efficiently on white box hardware and generate IPFIX flow records. It is designed to operate primarily on Unix-based systems (including Mac OS X), and is supported by the Network Situational Awareness team at CERT.
check_websites is a very simple virus scanner for Web sites. It checks a document root directory for files with the .js extension and for codewords which might be a hint of defacement or SQL injection. This tool is made to run as a cronjob. There's no output on the screen, but it generates a logfile and mails output.
Picviz is a parallel coordinates plotter which enables easy scripting from various types of input (such as tcpdump, syslog, iptables logs, or Apache logs) to visualize your data and discover interesting results quickly. Its primary goal is to graph data in order to be able to quickly analyze problems and find correlations among variables. With security analysis in mind, the program has been designed to be very flexible, able to graph millions of events.
The Cryptographic Implementations Analysis Toolkit (CIAT) is a compendium of command line and graphical tools whose aim is to help in the detection and analysis of encrypted byte sequences within files (executable and non-executable). It is particularly helpful in the forensic analysis and reverse engineering of malware using cryptographic code and encrypted payloads.