Hi muckamuck! 
Right now, “Highest Rated” comment organization is based on a combination of a comment’s overall goodness and civility ratings, as well as the number of likes the comment has received.  “Most Liked” comments are organized based on the number of likes received by an entire thread.  We’re working on smoothing out this organization system to make it more representative of information that you, as commenters, would find useful--so stay tuned! 
Hope this helps,
Lydia at Civil