Originally from Randy Marchany's post to ED-SEC 31 Oct 2006.
Vulnerability/Port Scanners
Nessus (mentioned in a previous note) is still the best even though their licensing has changed.
nmap - still the best of the port scanner, OS identification tools and builtin most Linux distros.
Active Ports - host based GUI version of netstat or lsof that attempts to map system processes to port listeners.
Configuration Tools
Center for Internet Security NG Tool/Benchmark for Windows - free from www.cisecurity.org. Provides a consensus benchmark and scanning
tool that compares system settings with the benchmark. Provides a numeric score showing what % of your setting match the benchmark
Microsoft Baseline Security Analyzer v2.0 - scans local and remote systems and provides a nice report of system settings.
Belarc Advisor - similar to MBSA but harder to find these days
Paros - excellent tool with spider capabilities, limited security scan capabilities, ability to freeze www transactions and allow for dynamic replacement of www strings. Also, does some minor cross site scripting tests.
WebScarab - available from www.owasp.org. Another good web security tool that allows you to replace session ID, cookie values to test web app security.
One Stop Shop
Backtrack (formerly Auditor) available from www.remote-exploit.org. This is the big daddy of toolkits. Standalone Knoppix implementation that contains most of the tools mentioned above plus a whole suite of password crackers, enumeration tools, wireless security tools and more. You need this suite to fully assess your assets.