"Highest Rated" is based on a combination of ratings received during the review process (that is, the answers to the "Is this a good comment?" question) and the number of likes it receives. You can also sort by "Most Liked" to see comments sorted by number of stars. 

Note, though, that we keep comments threaded, so if the most-liked comment is actually a reply, you'll still see the top level/parent comment first!