Agreed. Angerwhale (my blogging engine) has a feature for transcluding blog posts from other Angerwhale instances. So, if you want to comment on something, you can post a blog entry about it and then transclude the post as a comment. Then the comment thread from your blog becomes a sub-thread in the including blog (and so on recursively). That way, when you comment on a comment, everything ends up in the right place. The original post that everyone is replying to is the canonical source for all replies, regardless of whether or not they are "comments" or other blog posts.

Anyway, this is the Right Way as far as I can tell... but it appears that there are only 4 or 5 people in the world that use Angerwhale. Maybe I should make the mechanism compatible with WordPress or something :)

(BTW, I should mention that I like FriendFeed's solution to this problem better than Posterous'.)