Way back in October 2009 Reddit introduced their "Best" comment sorting system. We've just pulled those changes into Less Wrong. The changes affect only comments, not stories.
It's good. It should significantly improve the visibility of good comments posted later in the life of an article. You (yes you) should adopt it. It's the default for new users.
See http://blog.reddit.com/2009/10/reddits-new-comment-sorting-system.html for the details.
I found a Reddit thread explaining the different comment sorting systems. Does LW use the same algorithms for each method?
http://www.reddit.com/r/TheoryOfReddit/comments/1y8rst/what_is_the_best_way_to_sort_top_best_new/
Missing from their list though are "popular" and "leading" (and "old", but that's pretty self-explanatory). I'm guessing "popular" is the same thing as "hot", judging based on what appears in my address bar when I sort that way. "Leading" is listed as "interestingness" in the address bar, which leads me to think it adds weight to comments that inspire a lot of discussion. My observations suggest that it also factors in votes though. Could someone please clarify further on what these algorithms do?