Besides perlsec, the Camel has a chapter on security, although it covers the same ground.

Perl.com ran an article last year called Preventing Cross-site Scripting Attacks, which pertains to the area of CGI security, as does the O'ReillyNet article Beware SQL Injection in Web Applications. Both of these should make interesting reading for you.

Here are some more resources that I noticed are linked to from the Tutorials section of this site.

Please do not be afraid to ask questions specific to the area you are dealing with - it is obviously very important for you to understand this stuff.

MB

Update: Here is another article of relevance from IBM DeveloperWorks, published in February 2004.