It's a relatively minor use of Perl, but I constructed a script using Digest::MD5 to track and ensure integrity of my chkrootkit binaries. I'm using this as a double-layer of trust to make sure that nobody modifies the existing chkrootkit binaries (which, in turn, monitor my system binaries for rootkit activity).
One obvious use for Perl in a network security setting would be an IDS (or NIDS), where Perl's excellent pattern matching capabilities would help to match packet fingerprints, but this is already handled capably by the likes of Snort. Unfortunately, I just don't see Perl scaling to the same performance levels as Snort.
-fuzzyping
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