I think threaded comments would be a great addition. I get a lot of questions in my comments, to which I respond, but it's difficult to tell to which comment the response is directed. I had quoting the original question and wasting space, and editing the time stamp of the reply so it appears in the correct location in the thread takes too much time.
It would be great if all comments were threaded, and then let the theme decide how to display them (single level as it is now, 2-level, infinite level, etc.) You currently get to choose how the archives are displayed; it would be nice to have the functionality for comments.