For a while now in Disqus 2012, you can see that a comment was replied via the dotted dots and the "parent" text above comments. The parent text was a useful feature, with you being able to hover over the text to view part of the parent comment, and clicking the link takes you to the parent comment's anchor in the page.
There has been two changes in this version of Disqus 2012. First off, the parent text has changed from "parent" to "in reply to <xxx>" next to the name. The second change is with the @<screen name> text when someone replies to a comment that is more then the 4 level thread of the comments. After that, the comments maintain the same width, but had the @<name> of the user a comment was being posted to as reply. That is now gone is now replaced by the "in reply to <x>" shown in the previous image. You can see the changes below from a post about the periodic table.
Hope you all enjoy this change. If you also didn't notice, the "Mod" badge on moderator comments has changed from green to some form of a light gray. No word on that from Disqus, but lets hope that the ability to style those buttons via both text and color will come soon.