Almost all users use POPFile as a spam filter, most of them also use the fact that POPFile can sort in arbitrary categories of mail. However, some people have pushed POPFile even further... Martin Overton (of IBM) has used POPFile to discover email borne malware, even finding that POPFile could automatically detect mutations. Now, some researchers in Japan have used POPFile to detect weak encryption of email with 80% accuracy.
The researchers were building a system to detect improper sending of personal information by email. Their system first checked for the use of strong encryption (if the mail is strongly encrypted then there's no need to worry about eavesdropping), the system also checked for things like telephone numbers, email addresses and other personal data in non-encrypted mail.
But they also wanted a system to detect poor encryption (such as ROT-13), and for that they turned to POPFile. After a mere 30 emails had been trained in POPFile it was able to distinguish plain text messages from those encrypted with weak ciphers.
Some details in their paper.