Although I have recently switched to POPFile, I instantly found it to be simple, customizable and highly affective at sorting my mail.
I have a simple configuration with two buckets, spam and clean. After less the 20 mails spam was correctly being filed inside my mail client (I use a rule to route [spam] pre-fixed mails to a folder). I have created some 'magnets' which enables me to mark mails to a particular address as spam.
Any mail that get misfiled is a breeze to reclassify with the simple web interface. With all my mail in my mail client I can easily see what is right or wrong (wrong about 3 times so far).
This software does not automatically re-configure your mail client, but this is in the documentation on what you need to do (sub 30 second fix if you know your mail client).
A great piece of software that fits my needs a treat.
License: Free Details...