Like many others, I was hit hard by comment spam in recent weeks. This was compounded by the fact that MovableType doesn't have convenient interface for listing and deleting spam comments.
My solution: Disable comments. As this is not directly supported by MovableType admin. interface, I had to edit mt-comments.cgi file. This may be too drastic but I can't think of any other easy way to handle this in the short term. I will upgrade one MovableType has good safeguards in place.