I got a request in email to add something like Disqus to my blog, which would allow a richer platform for the commenting that goes on here. I think that the request and my reply are interesting enough to warrant this blog post.
My comment system is the default subtext one, but there are several advantages to the way it works. You can read the full explanation in Joel on Software post about the matter, but basically, threading encourages people to go off in tangents, single thread of conversation make it significantly easier to have only one conversation.
There is another reason, which is personally important to me, which is that I want to "own" the comments. Not own in terms of copyright, but own in terms of having control of the data itself. Having the comments (a hugely important part of the blog) being managed by a 3rd party which might shut down and take all the comments with it is not acceptable.
That is probably a false fear, but it is something that I take under consideration. The reasoning about the type of interaction going on in the comments is a lot more important. There is also something else to consider, if a post gets too hot (generating too many comments), I am either going to close comments on it, or open a new post with summary of what went on in the previous post comment thread anyway, so it does have some checks & balances that keep a comment thread from growing too large.