Coding Horror very recently had a post on threading: http://www.codinghorror.com/blog/2012/12/web-discussions-flat-by-design.html
I personally like threaded comments, as it lets you follow the conversation in just about any chosen direction.
It might work best here to allow threaded comments, but limit them to 1-2 levels deep.
Thanks for that link @BlueThen, the discussion on HN is also quite good, http://news.ycombinator.com/item?id=4919111
I can see both pros and cons for changing it to threaded. Tbh for our current userbase it would be better to have it flat IMO. Although @BlueThen has a good point about 2 levels deep. First level is the initation of subject in response to the post, second level would be discussion on that. We would need a lot more users for a complete threaded system to be the best option, though.
The main reason I asked this was because I've been getting questions on my more popular snippets that aren't really relevant to most of the commenters. When I reply I feel like most people don't need to see my response. This can be partially remedied by not sending a notice when a comment starts with a @mention, but a single level deep thread might also work. I think for now we'll stick with @mention replies.
@Conscious Been getting lots of questions here: http://www.hawkee.com/snippet/9391/
I had an idea. Maybe I can use the same homepage interface for code snippets and projects. It would be a most-recent-on-top single level deep commenting system. So you would post a new comment thread by clicking what is now the status update link and each new comment would act like a status update where it can have multiple replies, but only a single level deep.
If users treat it properly it should be clear. In a way it would act more like a forum where top level comments are topics to be discussed. The more I think about it the more I like the idea. It would allow for much more detailed discussions which would fill the void left by GitHub. There projects don't allow for discussion. Ultimately I'd like Hawkee to be the discussion arm of GitHub where developers can discuss potential features and get feedback from their users, much like I'm doing right now with this discussion.
I ultimately decided to use 1 level deep comment threads and have completed the change. Here is the changelog, http://www.hawkee.com/status/102009
I like that idea. Maybe go the extra mile and do something like the "Reddit Enhancement Suite" add-on does on reddit. It colors the background to make the comments/replies easier to follow.