I'm most proud of the code I wrote in 1986 to monitor fish in real time, so they can be used to detect water quality changes. It's still in use.
http://news.google.com/newspapers?id=HNwfAAAAIBAJ&sjid=WNkEAAAAIBAJ&pg=1499%2C696260
My favorite perl code was a bit of munging I wrote for someone literally halfway around the world, to interpret GPS logs to prove illegal fishing took place.
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