POPFile
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POPFile is a free, open source, cross-platform mail filter written in Perl by John Graham-Cumming. It uses a naive Bayes classifier to filter mail. This allows the filter to "learn" and classify mail according to the user preferences. Typically it is used to filter spam mail. It can also be used to sort mail into other user defined "buckets" as well (e.g. the user may define a bucket for sorting work email).
The program works by setting itself up as a proxy between the email client and the POP3 server. As mail is downloaded via POP3, the filter identifies and classifies mail and makes a user defined modification in the subject line with name of the bucket that the mail falls into. The user then sets up rules in the mail client to sort the mail based on the subject line modification. If the user sees that mail has been placed into the wrong bucket he or she can use an HTML based interface to instruct or train POPFile about the correct bucket the mail should have been classified in.
As an alternative to the subject line modification (or as a supplement to it), the system can also be configured to use custom mail headers instead.