It seems that the highlighting we talk is not the same thing, it is a bit hard to explain, but check this demo: http://tout.essaye.sauf.ca/tribune

The module has a notion of threads based on timestamps: typically, a user clicks on the timestamp at the left of the message they want to answer before typing their message. When the messages is displayed, hovering the mouse over timestamps highlights the corresponding references and answers

http://drupal.org/project/tribune