Are you running bayes and getting a lot of bayes_99 hits? If so, the score for bayes-99 is a lot lower in 3.0. This has caused problems for some people.
Alternately, do you *think* you are running bayes, but maybe it isn't working? The database format changed and you need to upgrade it forward for bayes to work. spamassassin -D will tell you if it is working and trained. Have you run lint to make sure that all of your rule files are good? Things changed since 2.6x, and SA is picker about what is valid and not. So it may be tossing out a whole lot of your local rules if you have some syntax errors. Loren