I asked last week
http://news.ycombinator.com/item?id=1006946
whether attempts to make the site better, which is what many downvotes and flags currently are, ought not to be rewarded with MORE karma rather than less. I think people who clean up the trash should be paid for their work.
It seems to me, respectfully, that using the downvote to try and clean the community is like a small-town sheriff trying to keep the perceived riff-raff of city-slickers, with their strange ways and funny hair, out of his community.
I think a bigger danger is the suppression of dissent. Rewarding it with more karma would be a huge mistake.
By the way, it's an EMPIRICAL question whether downvotes or posting disagreeing replies does more to discourage expressions of certain opinions. It seems to me that someone thin-skinned enough to cease posting his opinions because his comments get downvoted (rather than reconsidering how he comments and seeing if he can improve how he comments) might be just as discouraged from posting minority opinions if he sees a lot of replies that disagree with him. If a person has courage of his convictions because his opinions are based on evidence and careful thought, there is little reason not to come back here and express the opinions, even if his comments don't get a huge number of net upvotes.
I respectfully disagree. A downmod supplies almost zero feedback to the recipient. Many posts I've seen with negative mod scores are complex and have a number of topics in them. A downvote at no time explains what precisely was wrong with the post.
It's like a presidential candidate not getting a vote, he doesn't know what part of his platform lost him the vote, just that he didn't get it.
In real life a candidate can pay for a poll and find out why, here it seems that asking why immediately results in more downmods.
(I admit the analogy is imperfect, but hopefully you see where I'm trying to go with it).
And meta-comment, really? Your post was downvoted? Way to discourage ideas and effort....sigh
Perhaps a way to balance this is making flagging (up or down) cost karma points, but that would lead to them (KPs) being visible to give immediate feedback on the user's actions. Likewise, upvotes give back the karma you lost modding some comment. A different cost for up/down seems also a good idea. This, simply, could create an incentive to post even when one has nothing to say and prevent constructive modding by people who post little.
Hmm.... Perhaps an agreeing vote would redeem part of the karma paid to up/down vote.
This balancing act is a very hard problem.