Ah, but how do you count that in a ranking algorithm? I'm 90% sure my idea is not the answer, but maybe we can think of something else.
Maybe this is naive, but there's something about a binary voting system that just strikes me as something that doesn't fit into a conversation. I often find myself agreeing with certain parts of a comment and not other parts of it. Maybe if the user could vote up the parts of a comment he likes and vote down the parts that he doesn't. Technically, that would be difficult (especially since on HN a comment is simply a text field).
Have you ever considered giving people the option to register their abstinence from voting on a comment? Right now we have up and down, but a lot of the time I feel like I wish I had an "abstain" button. This would be reserved for the comments that aren't mean-spirited, but don't add much to the conversation.
Then perhaps a comment with 20 up, 5 down, and 500 neutral would rank lower than a comment with 20 up, 5 down, and 0 neutral. The idea being that, all things being equal for two comments, the one with more indifferent voters is considered less valuable, and is thus ranked lower. Maybe a neutral vote simply works by increasing n when judging the size-weighted score that HN uses to calculate rankings now.
I'm sure there are flaws in this line of reasoning..perhaps someone would be so kind as to point them out?