Originally when I made the comment system here, I wanted just registered users to be able to post in order to prevent spam. Eventually I decided to allow anonymous comments because someone might have something to add to the discussion without wanting to either login or register in order to do so. Then the spam began, but eventually I found some good methods of stopping it. But I made sure to keep a clear separation between registered user comments and anonymous comments. Registered users got their own section above the anonymous commenters, so if some spam were to come through, it would be at the very bottom anyways, and wouldn't screw up any ongoing discussions.
But I found myself wanting to be able to respond directly to anonymous commenters without having to refer to them by a number, and also to allow anonymous commenters to leave comments where they are relevant in a discussion. I think between some automatic measures as well as my own policing of the comments, spam shouldn't become an issue.
To maintain a distinction though, registered users still have their comments highlighted more brightly/boldly than anonymous users, and I encourage registering if you comment often since then you will have a user page where you can track your comments and submissions.
See this week's Entourage review for a good example of what it looks like now. As usual, let me know if there's any bugs that got introduced during the change.