nofollow breaks trackbacks, and what Firefox users can do
Let's say you create an entry on your blog that comments on this post. You give a link to this post and send a trackback*. That's the way trackbacks are supposed to work: they create a reciprocal link between two posts, each referring to the other.
But, let's say I was sneaky and I didn't really want a reciprocal link, I just wanted a one-way link from your site to mine.
What I could do is use a "nofollow" tag on the trackback link pointed back to you. While people might click on that link, search engines will ignore it. So, you've given me a nice link that search engines will follow, but I'm not returning the favor.
And, this appears to be MovableType's out of the box behavior with their latest versions. Most bloggers probably have this setup because they don't know better, but I'm sure there are more than a few who know what's going on.
If you use Firefox, you can install the one-liner described here in order to easily detect sites that use nofollow: those links show up as red text on a black background.
* Note: I've disabled trackbacks at least for now, but I don't use nofollow on other links left here.