NOTE: The following was written very early in the morning on very little sleep. It might have come off sounding very bitter :)
Until recently, I was not exactly sure what the rel="nofollow" attribute of a link did. I had seen it discussed briefly on other blogs, but never really looked into it. I just came across it again, so I figure I would look it up. On the Google blog, it is described as such:
If you're a blogger (or a blog reader), you're painfully familiar with people who try to raise their own websites' search engine rankings by submitting linked blog comments like "Visit my discount pharmaceuticals site." This is called comment spam, we don't like it either, and we've been testing a new tag that blocks it. From now on, when Google sees the attribute (rel="nofollow") on hyperlinks, those links won't get any credit when we rank websites in our search results. This isn't a negative vote for the site where the comment was posted; it's just a way to make sure that spammers get no benefit from abusing public areas like blog comments, trackbacks, and referrer lists.
Sorry for my bluntness, but this just feels like load of horse crap to me. Am I crazy? This seems to like treating the symptoms of a disease but not the causes. Linking in your comments is NOT a problem; that's why we try our best to auto-link URLs within the content. The problem here is anti-spam techniques. Get those better and you won't have to worry about where the links point to.
And as far as:
...those links won't get any credit when we rank websites in our search results.
... is also bogus. People put a LOT of time and thought into their comments. I am lucky enough to have awesome people who place comments on my site that are some of the most well thought out, amazing explanations that I have ever read. If I was to then turn around and tell them that their effort will not get rewarded by linking credit, I would feel like a disgusting person.
If you are so worried about every little thing that gets posted to your comments, then moderate them... don't stop them from working "properly".
My two cents!