Late last week Jay Allen, the designer of MT-Blacklist posted recommending a plug-in called MT-Moderate and some other anti-spam tools. MT-Moderate originally force-moderated comments, which is basically one of the things that MTB does, but it has been redesigned to force-moderate trackback pings too. That was a privacy hole in MTB (and MT) which doesn't have a trackback moderation feature. Some blog spammers send pings - usually in large waves. If they managed to evade the MTB blacklist scan, the pings got into the public site. Spam comments that got around the blacklist, on the other hand, usually ended up in moderation.
I have installed it - following the instructions to set it up for Trackbacks only (to avoid overlapping and weirdness with MTB). It works. I still get trackback notifications but the pings are moderated. I can then use the MTB despam functions on the moderated pings to update the blacklist and delete the ping from the database. Nice.
MT-Blacklist is a good stable and useful program. It's a plug-in and it seems to be available on a free open-source basis for Movable Type Users. Jay Allen has a day job, and he hasn't been revising the program over the last couple of months. He has written about spam on his own blog and I think he wrote or contributed to Movable Type/Six Apart's online Guide to Combatting (Comment) Spam.
Did you install it without the comments.pm file, so as to avoid duplication of comment moderation with MTB? Ah, wait a minute, that info is in the documentation.
Jay Allen is a great guy, I've corresponded with him on a couple issues.
At some point, I want to replace my PBD template with something compatible with MT 3.x