I upgraded to Eudora 6 awhile back, and I've been mostly happy with it. The spam filtering seemed mostly good as well, until recently - when I started noticing that scads of good mail was being junked. I spent the last week or so fishing things out of the junk folder, until it finally dawned on me that maybe there were settings for this. Lo and behold, there is.
It turns out that Eudora assigns a "spam ranking" to each incoming mail - a number between 0 and 100. There's an option to set the minimum ranking before having something get junked, and that was unset. I'm hoping that setting that will result in fewer lost messages.