Generally if I'm auditing a piece of Perl code for security, the first thing I do is check for -Tw on the command line, for taint-checking and warnings. I then move through the source and look for instances where they're un-tainting something, and be sure they're doing it properly.

If your code passes muster here, I would be tempted to rule it secure from a CGI point of view. Obviously there's more to it than that, but simply ensuring your script runs well and without problems with taint-checking and warnings turned on, I feel a lot better about it.

If it doesn't, then you likely have problems.