Nikto is an Open Source (GPL) web server scanner which performs comprehensive tests against web servers for multiple items, including over 3200 potentially dangerous files/CGIs, versions on over 625 servers, and version specific problems on over 230 servers. Scan items and plugins are frequently updated and can be automatically updated (if desired).
Nikto is a good CGI scanner, there are some other tools that go well with Nikto (focus on http fingerprinting or Google hacking/info gathering etc, another article for just those).
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