History
June 6, 2012: Fixed an issue that can cause major problems with chat.
December 17, 2013: Fix an incompatibility with the Winter Bash code.
Screenshot
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About
Instead of showing comments in chronological order, this user script displays them in a threaded view, making it easier to follow conversations in long comment threads.
It uses heuristics similar to the @-reply recognition (but it is a little bit more flexible).
It should be noted that this may obviously change the order in which comments are displayed, so you cannot rely on a chronological order anymore. In most cases this doesn't matter, but sometimes it just might.
Update 2011/07/10: As suggested by George Edison, now offers a button to undo the threading on a particular post, in case you want to see the comments in their regular order. I'm not 100% happy with the UI, but I guess it's good enough. The script also got a little smarter about finding the replied-to comment.
Download
install / update script – view source
Platform
I have tested this script in Chrome (Windows 7), Chromium (Fedora 14), and Firefox + Greasemonkey (both OSes).
Contact
This script is created by Benjamin Dumke-von der Ehe. Note that this is a free-time project of mine, and has nothing to do with my employment at Stack Overflow. See my profile for contact details; you can also often find me in the Tavern on Meta Stack Exchange chat.