I've found another way to limit comment spam on my site, with the ThrottleSeconds variable and some modifications suggested by Phil Ringnalda and Jacques Distler.
With the 2.66 editions of Movable Type, there is a ThrottleSeconds parameter one can add to their site that limits time between posts from the same IP address to deal with people who automatically send junk to your comments. The default value is 20 seconds.
To enhance this, Jacques Distler posted a patch for Comments.pm that expands this to limit the total number of posts per hour and per day. This helps you deal with the worst of the bunch that have figured out how to change their IP address every so often.
To make this even more flexible, I created some additional Throttle variables and modified Distler's code to use them. To do that, one needs to add the variables to their mt/lib/MT/ConfigMgr.pm file. These can then be used in the mt.cfg file at will. (If you just put them in mt.cfg, you get an error about the new variables when any script runs.) I'm happy to give you a copy of my changes.
Additional very good background on comment spam from Elise.
Note: MT appears to be particularly susceptible because it is so widely used and the factory spammers have discovered how to run scripts on their machines that post comments to the blog with frightening frequency. Other blog tools have this problem as well, and people are working to make it more difficult to flood spam onto a site.