We're still in beta and the trolls have come out of their caves. I suspect in the weeks and months to come they will multiply like rabbits. The subject matter at hand is going to breed them like there is no tomorrow.
It looks like this: You put up your great-well-researched-answer. You are passionate about it and you think you explained it well. There are other answers along side yours with dissenting views, but all is hunky-dory until the inbox alert lights up. You have a comment. Rejoicing that somebody thought your post worthy of feedback, you click through.
Inside you find the greasy slobber that a cave troll left after devouring your answer with no appreciation for its finely spiced arrangement of dishes.
Your frustration boils -- he didn't even read your supporting text, he just objected to the premise. The trolls own philosophy isn't clear and the premise of his objection is untenable. However answering him properly and setting the record straight would take much more than the 600 character character limit on comments.
What other options do you have? His comment hasn't said anything personally offensive, he's only insulted your viewpoint not your person so you can't flag it. He hasn't posted his view in an answer himself so you can't down-vote it based on it's lack of merit.
You remember the adage Don't feed trolls, but what option do you have but to fire off a reply? What are the options other than firing off a comment to say that he's still in the dark ages?
TL;DR: What is some sage advice for dealing with comment trolls?
(Links to other meta sites where people have experience are welcome.)