I understand this ages old bug is never brought up because vast majority of WP installations are on small sites without heavy community participation. As a webmaster with a high traffic WP based site that gets on average one new comment per minute, I have been bothered by this quite serious bug for a while. Here's what the problem is:
If an abusive comment is made and admin removes it, the order of display of all comments in the post made after the deleted comment is disturb. In the admin area, comments made as replies to other comments show to have been made as a reply and show to which commenter, but on the actual post, they are displayed as a stand alone comment in random order. Basically, every single comment after a deleted one is misplaced, displayed in random order, and if it was a reply, it's not "nested" within its parent comment.
I may be the only one who experiences this because I get a lot of comments and a lot of abuse which requires removal of comments, but it's still a serious bug that needs to be addressed. It has been ignored for many releases. Will it be addressed soon?
If a developer wanted to see what exactly it does, I can show it to you on the live site. You will see in admin area that the comment is made as a reply to another comment and should be nested, but isn't. Or that one comment was made later than others but is displayed before them. This once again only happens when there is a delete comment in the post. The deleted comment affects all subsequent comments made on that page, so it's not that comments made as a reply to the deleted comment are misplaced. All made after the deleted one are.