I have found a way to backup and/or share the "brains" from the Junk filter in Mail.app. Recently, I wanted to wipe out my system and reinstall a fresh OS X. I didn't want to back up and restore my user directory (defeating part of the purpose of a fresh install) but I didn't want to lose over seven months' worth of Junk filter training.
The solution is a single file: ~/Library/Mail/LSMMap. Simply back up this file, and when you reinstall the new system, run Mail, reconfigure your mail server(s), and turn Junk filtering to automatic. Quit Mail and place a copy of the backed up LSMMap into ~/Library/Mail, replacing the version that is there (about a 1.2 meg file). That's it!
The Junk rules can be shared among multiple computers in this way as well, provided you match up owner and permissions on the destination machine.

