The conversation often continues in the Comments and important information is held in the comments. I'd like to have threaded comments there. It would make it easier for people who are editing answers to be able to see the real useful information in the comments separately from the conversations that occurs in the comment stream below each answer.
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Jeff really hates threaded comments. Personally I like them - when represented in a useful way, with easy ways to mute/highlight appropriate subthreads, but I doubt that we'll ever see them on SO.
Having said that I like them, I'm not even sure they'd be appropriate for SO anyway, which is more designed for Q&A than discussion. Sometimes I wish there were some way of leaving the questions/answers as they are, but launching a new discussion (with threading) where suitable. Can't see it happening in the near future though.
As Jon seems to address, threaded comments are great for following discussion. Jeff has said before that he explicitly wants to avoid discussion on SO, so if threaded comments help discussion, it would seem that adding threaded comments would, in a sense, be giving a blessing of sorts to discussions on SO. It's nice in theory, but it goes against the current mission of the site.
I do like the idea of a discussion area, though. Often times, I have a question or discussion topic that I would very much like to bring in front of this particular community, but it's not necessarily programming related. Sometimes you want to ask your "work peers" questions not necessarily related to your "work."
Threaded comments would be useful.
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Threaded comments and threaded answers would be great - for another site.
On this site, it would just encourage discussion, which is discouraged.
I truly wonder why discussion is so discouraged herein. Some answers can be very difficult to get at and discussion about the answer could help a really good answer to emerge instead of having an endless list of partial answers or a hard to follow comment stream that needs to be completely followed through to get at the real juice.
On the other hand, I realize that many questions in the Stack Exchange sites are simple enough and warrant that a single right answer can do it.
A certain form of argumentative questions can be supported through the wiki mode. Perhaps having threaded comments only in the community wiki mode would be of great help in getting these hard questions to emerge. Since there are no reputation points involved in community wiki mode, editing them also solves the difficult task of assigning proper reputation points though there are some solutions to this.
It is true that arguments can be difficult to manage and often degenerate. That said, the community participating in the Stack Exchange sites is thus far very disciplined in this regards and seldom stray off topic. Yes, sure you can find plenty of examples where things just went wrong, but overall it is the exception.
Stack Exchange sites have gone a long way since their inception and are quickly becoming THE reference in many subjects. But it still lacks a certain depth, discouraging discussion certainly helped with the discipline, but it also gave the community a glass ceiling, shackles of sorts, that prevents more difficult answers to emerge on some questions.
In short, encouraging argumentation and discussion at large would most likely not be a good idea. But allowing some question to generate discussion and providing a specific UI enhancements to support discussion would benefit the whole community. Perhaps Community Wiki is the way, but perhaps a new mode of providing answers would be required to support argumentation in a constructive way.