having more points puts you at the top of the comment list.
So, for example, this comment will have one point when i first post it. Since it's the latest comment, it will at first display topmost. When the next person posts a comment, my comment will display last and his will display first. Then when I refresh mine will display first and his last.
Not that I'm suggesting that a SQL database backs news.yc; pg seems to have a preference for filesystems over databases.