If you have an issue with a lot of comments (e.g. JRA-4446) and you are reading the most recent comment at the bottom, you have to scroll all the way up to the "Comment" link on the left sidebar. This adds a comment window at the bottom of the page. If you are responding specifically to a comment that is not the most recent comment, it's not easy to link to that specific comment (yes, you can copy the permalink, it's a pain) or to see that comment while you are typing a response.

Please add a "reply" link to the Edit | Permalink | Hide menu on comments, to make it easier to reply to a specific comment.