I think I feel the problem is more a mismatch between the subtlety of the problem and the bluntness of the tool. Downvotes are a harsh and low-signal way of pointing problems in arguments, and seem more suited to punishing comments which can be identified as crap at a glance. Since this site isn't doing the free-for-all comedy club thing Slashdot and Reddit have going, I'm not sure that the downvote mechanic quite belongs here to begin with. Users posting downright nonsense and noise don't even belong on the site, and bad arguments can be ignored or addressed instead of just anonymously downvoting them.
And yes, this probably should go to a toplevel post, but I don't have the energy for that scale of meta-discussion right now.
Downvoting wrong comments may be harsh for the person being downvoted, but hopefully in the long run it can encourage better comments, or at least make it easier to find good comments.
There may be some flaws in the karma system or the way it's used by the community, but I don't see any obvious improvements, or any other systems that would obviously work better.
Look at mwaser: he complains a lot about being downvoted, but he also got a lot of feedback for what people found lacking in his post. Yes, a portion of the downvotes he gets may be due to factors un...
[Update: and now there's a fifth discussion thread, which you should probably use in preference to this one. Later update: and a sixth -- in the discussion section, which is where these threads are living for now on. Also: tag for HP threads in the main section, and tag for HP threads in the discussion section.]
The third discussion thread is above 500 comments now, just like the others, so it's time for a new one. Predecessors: one, two, three. For anyone who's been on Mars and doesn't know what this is about: it's Eliezer's remarkable Harry Potter fanfic.
Spoiler warning and helpful suggestion (copied from those in the earlier threads):
Spoiler Warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.