The battle against comment spammers seems to be never ending. The latest craze is to flood a MovableType based site with comments or trackback pings, similar in effect to a DDoS attack. MT responded with a change that attempts to throttle the number of comments received over a period of time. Ironically, installing MT-Blacklist, which is an attempt, albeit not the most robust, to stop comment spam, inactivates the throttling code. But I digress.
This site attempts to show how to get these two working together and offers links to other resources to help reduce, but not eliminate the problem. I guess this is the best that can be hoped for, short of turning off comments completely.
