The W3C World Wide Web Security FAQ, esp. Chapter 6, CGI
CGI Programming with Perl, 2nd Edition, Chapter 8, Security
Writing More Secure CGI Scripts
Security Issues in Perl Scripts

and many more. Google is your friend here.

Oh, and before someone considers the link to O'Reilly to be copyright infringement, it's a free sample chapter from the O'Reilly site itself.