Environment: MacOS X 10.3.2 and Mail.app 1.3.2.
Experience: Junk mail filtering stops working, and when manually classifying mail as Junk, Mail.app crashes.
Workaround: Quit Mail.app, delete the ~/Library/Mail/LSMMap2 file, then relaunch Mail.app.
Source: Post to Macintouch.
This has happened to me several times on the laptop, and now on the desktop. I just now tried the tip above, and it works well, although I did wonder, briefly, what deleting that 1MB file would do, and whether I should save a copy. But I depended on the accuracy of the Macintouch post, and I was not disappointed. Thanks to Allen Cronce.