Here's my proposal. Every comment has a 'Reply' link after it. Clicking on this link adds the standard @UserName: to the comment edit box.
After posting, the @UserName: is converted into a javascript 'link'. By 'link' I mean that it appears to be a hyperlink, but is actually a span with the hyperlink style and javascript in its onmouseover event. When you hover over this link, the comment it references is highlighted in some fashion (background color changes, its outlined, whatever).
When the referenced comment is hidden, one of two things can happen:
- The comments section is expanded and unshown comments are revealed, or
- A hovering div appears next to the pointer containing the comment that is referenced.
No. 2 is probably easier to implement.