I think many readers will be happy to find out that we have implemented the oft-requested comment threading. Threading comes in two modes: "Collapsed," in which you can view a linked comment title beneath a parent comment, and "Expanded," in which you can view the entire comment, associated via indentation. Here is some detail on that.
First off, threading is only available to registered users. This will not change - the editors all agree that threading is an incredibly unfriendly, illogical, counter-intuitive system for tracking comments for those not familiar with it. Although it may seem to make sense, it carries several drawbacks.
1. Threading does not provide an easy way for a user to decipher which comments have been added since they last visited the site. Currently you must either remember it or somehow divine it. This is the largest drawback, I believe, and the only way around that is to track which comments you've seen or to provide that information in a cookie. Since we know that several of our tin-foil hat wearing users do not like cookies, we are forced to track the information ourselves, and its not in our best interest to additionally hammer the database until v3 optimization is complete. Either way, I think everyone agrees it's unreasonable for a large website to track user views for each story, even if it's simply the highest number comment you've seen.
2. I experimented with "reparenting," which is displaying a reponse to a comment which has been voted below your threshold. I found it to be more confusing than anything else, as it was not immediately clear that the comment was a reply. Instead, collapsed parenting has been added, which means that comments below your threshold are ignored unless they have replies which are at or above your threshold, in which case they are collapsed. Doesn't that sound really confusing? That's why we've avoided threading for so long, because those of us who know how to use it often forget how much assumed logic there is in deciphering what one sees.
3. Because of the basic usability design of the site, it is not easy to provide a consistent interface that can accurately capture all replies without making the comments per page variable. This means the first few pages are likely to be very long as the replies will always be higher, and the last few pages shorter. I'm looking into ways to fix this disparity, but I don't think it can be done without rewriting large portions of the comments engine.
For these reasons and more, threading is neither extremely practical or usable enough to be our default interface. We provide it solely as an alternative for our registered users. I can tell you after using it for a few days, it's very useful, although not always as easy to use as flat view.
For those who are wondering, I intend to add an on-the-fly view toggle to the comment page, although it will almost definitely rely on a cookie. If cookies are a problem... well, you have your preferences page.
Lastly, and perhaps most importantly, the threaded view has not been fully tested in all browsers. The threaded view has been tested in Gecko (Mozilla/Firefox), Opera, MSHTML (IE), and KHTML (Safari/Konqeror). Please consider all other browser support experimental. Additional browser support will continue to be added over the next days/weeks.