I discovered a spam fighting utility called POPFile through a post over at TechReport today. It's a tool that runs on your local computer and acts as a POP proxy between your mail client and your ISP's POP server. You reconfigure your mail client to connect to your local machine, and when you check mail, it queries POPFile, which goes out to your ISP's POP server and grabs the mail. Then it does some kind of analysis (probably Bayesian) and forwards the results to your mail client. POPFile also runs a local web server that's used for accessing retrieved mail for training the filters, and configuring POPFile.
Mail is sorted into what it calls buckets, which in Eudora-speak would be analogous to mailboxes. You can set up magnets, which are filters that file message directly into a particular bucket based on an email address or domain for example.
The training process looks pretty simple. Just a matter of connecting to the local webserver, selecting the messages that need to be reclassified and reassigning them to the appropriate buckets. POPFile adds a couple of headers to the message, which should make it pretty simple for your email client to do any secondary filtering afterwards.
Since most of my spam seems to come overnight while I'm not at work, I'll have to wait until tomorrow to see how effective it is out of the box. Earthlink's Spaminator supposedly catches a good portion of the spam I get, but lately it's been sucking. The amount of spam getting through Spaminator has pretty much doubled over the last couple of weeks, and seems to be slowly increasing. Hopefully POPFile will help with this after a little training.