While social networking for a client, I saw this nifty new "reply" feature in regards to comments left on a status update for fan pages.
In this case, it was visible on the Lawrence Public Library but I couldn't find it on any of the other Facebook pages I administer or ones I checked from my personal account. I think it's a good idea for a feature so you can directly respond to a specific comment to a post. It will most certainly help organize the thread visually.
Have you seen this option yet?