In a current posting from SANS (System Administration, Networking, and Security) they state "Vulnerable CGI programs and application extensions (...)" as the second most critical internet security risk.

One of the remedies they offer is - surprise - "Write safer CGI programs", and they recommend the following links:

http://www-4.ibm.com/software/developer/library/secure-cgi/
http://www.cert.org/tech_tips/cgi_metacharacters.html
http://www.cert.org/advisories/CA-97.24.Count_cgi.html

As of now, I didn't check those myself, but maybe someone finds them useful?!

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