Have been thinking about this for a few days, with the ways my content is cross pollinated across a number of different sites there are a number of ways readers can comment.
The most obvious one is on the article itself, here’s an example post which got some comments:
There is of course Twitter, where you can @reply a comment on articles because whenever I post an article, a Tweet is created to alert my followers that I have posted a new article. Here’s a comment I got recently:
Next is Facebook, as I mentioned above, when I publish an article I Tweet saying so, these Tweets feed into my Facebook status which again alerts my friends that I have posted. And the way Facebook now works you can comment on people’s status, here’s a couple I got on a recent article:
There is also Friendfeed, but I don’t use that much at all so I doubt I have had comments there.
I may put some more thoughts to this and try and explain why / who comments through which media, for now, which is your preference?