MovableType just released version 2.66, which includes a stopgap feature to help with comment spam. In 2.66, MovableType now includes a setting that prevents the same IP address from posting comments with the "N" number of seconds set. It also changes the way URLs are embedded in comments (by implementing some redirection), so that spammers don't enjoy a page rank boost from search engines by posting their URL over and over again.
Of course, MovableType 3.0 will supposedly include a comment registration system that will put an end to automated spamming.
Read: MovableType Update Provides Stopgap Measure for Comment Spam