Reputation for comments?
Should you gain reputation points when someone marks your comment as a "great comment"? Currently no points are gained in that situation. I think great comments should be rewarded.
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No. Comments are not meant to contain the meat of the site. Rewarding them with reputation, especially since many are merely humorous, will only result in a glut of comments from people only interesting in the rep they might possibly get.
Further, once you start gaining rep, someone will eventually complain that they can't downvote comments, and since they give rep that's important, and it'll blow up from there. Suddenly we need more moderation on comments, and people are penalized for funny or lighthearted comments because they "matter" now.
Leave them be.