DailyKos.com is a very successful threaded forum.
Actually I think this page itself shows that flat discussions donât work well if too many people leave comments and the discussion grows too large. Hereâs why:
I thought this blog post was interesting, and wondered âwhat do people think about it?â. However, I didnât read many comments on this page (flat discussion system), to find out. Instead, I read peopleâs opinions @ Hacker News (a threaded discussion system â which discusses this blog post) (here http://news.ycombinator.com/item?id=4919111 )
On this blog post page, there are too many comments not sorted in any particular manner (well, by date, but thatâs somewhat random, when people happen to find the page?). If I start reading, I think Iâd have to spend quite some time, before I find the âmost insightfulâ comments (which are the ones Iâd like to read). However, @ Hacker News, comments are sorted by votes, and I only need to read a few posts, to find insightful comments on this blog post.
I think flat layouts are geared towards writers â I mean, those who actively participate in the discussion, and read all comments. Then flat/threaded doesnât matter much, since one reads everything anyway.
Threaded layout, with comments sorted by votes, however, might be more geared towards readers. Readers are generally short of time and just want to be served the most âinteresting/usefulâ comments, read them and then go on doing whatever they need to do. Then it makes sense to let those comments surface to the top of the page.
Thanks for an interesting blog post 
I absolutely agree with this- threaded discussions drive me batty. But I mostly love that you quoted Parappa!
Hereâs the backstory for the picture : http://www.reddit.com/r/pics/comments/14stwl/my_sister_posted_this_picture_of_me_to_imgur_i/c7g3gks
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But, it will be a sad sad world when you canât keep a joke going on Reddit and Tumblr. Some of the most hilarious, clever, brain-bending things Iâve seen have come from those sorts of discussions.
The below link shows a version of Threaded Messages which is my favorite. The graphics are distinct, and navigation is aided by having a kind of 'index of linksâ at the top of a topic page that only contains the particular titles of the responses. (this site has been removed, but with a little experimentation you can get most of the links to work thru the Wayback Machine)
https://web.archive.org/web/20120613235757/http://forum.myredbook.com/forum/pool
I have to agree with @WillN, classic threading with separate tree view, threading by indentation, chronological flat, flat with @ or # references, auto-collapsed weighted threading, Q&As with comments etc. all have their appropriate uses, but as it happens ever so often, the wrong tool is used for the job. Discourse isnât perfect either (e.g. if I read direct replies to a post they should be collapsed in the main stream and parts that have been quoted in any reply should be marked in the original), but by default it fits more cases than most other approaches.
One thing that hasnât been mentioned yet, it seems, is an alternative and much more compact way to display the separate tree view: thread arcs.
Thread maps, that had been mentioned by @Zestyping, may work in (small) touch-screen UIs with vertical and horizontal swiping, showing a single post at a time.
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Another thing that hasnât been mentioned is this (hybrid?) design at www.drewgl.com which uses a flat design mixed with a visual map. Conversations are threaded but âmappedâ onto a flat display. Its difficult to describe, definitely worth taking a look.
To avoid long threads from indenting too far to the right edge of the screen, indent replies ONLY when the parent message has elicited TWO or more direct replies. If the parent message has only one direct reply, display all the replies in flat format below the parent message. When the parent elicits a second direct reply, nest the first direct reply one indentation below the parent message, and display all the subsequent replies to the first direct reply in a flat format.
Nesting is absolutely essential when one needs to elicit multiple and direct responses to a given post to serve mutilple functions. For example, when someone posts a major premise to support a proposition, we would like ideally one reply to test the relevance of major premise, a separate and direct reply to test itâs accuracy, another reply to test veracity (presenting evidence) and another reply to discuss its validity (logical soundness).
The problem with large spacing between the direct replies as threads and subthreads grow in size can be resolved by giving users the option to collapse threads at any select thread level (e.g. show only thread levels 1 and 2 to show the proposition in thread level 1 and the postings at level 2 that test each aspect of the stated premise.
It can definitely break down when you are starting a kitchen sink topic that can cover many wildly different scenarios, but then a) donât do that, as a general rule and b) if you must do that, use âreply as linked topicâ so the tangentical topics are linked together, forward and back:
This can be triggered in Discourse, for example, through the link button on each topic.
Another situation where you want multiple threads posted in response to a message is when the message poses a question such as âwhat are the possible reasons to support the claim Xâ. Each thread presents an unique argument to support X and all subsequent replies within the thread are intended to question, challenge, develop, establish that validity of the specific argument.
When we talk about the use and the advantages of flat versus threaded discussions, we need to talk specifically about the tasks and the nature or demand characteristics of the tasks that we wish to accomplish with discussion forums.
Allan
For example, this discussion should be broken down into multiple threads - one thread for each type of discussion-based activity/task (e.g. question-answer, debate, etc.) - to identify the unique advantages of each format (flat vs threaded).
Allan