Generally:
- Upvote posts and comments I'd like to see represented, are insightful, and/or make me think.
- Downvote: posts against HN guidelines (either in source material or the submission contents, e.g., editorialised title, duplicate submission), comments which don't add to the discussion.
I've been making a point of upvoting what I read as sincere substantive engagement even where that disagrees with me. One aspect of HN I find frustrating is that there's rarely much by way of substantive discussion, and HN's own systems often read that as a flamewar (e.g., a thread that's nested deeply and shifted far to the right). That's often the case but is not always the case.
With time I'm finding myself more favourably inclined to systems that have "flat" discussion threads. Google+ was one of these, and effectively each response was simply appended to the end of the thread. Conventions of mentioning an earlier reply and quoting a small bit of context emerged. The dyanmics and mechanics of posts differed from HN: there was always a directly-involved moderator (effectively), the post's own author. Whether or not that author would moderate, and how fairly they did so, of course, varied tremendously. People who were good at this, though, often had excellent discussions.
Threads were capped at 500 comments. Good discussion typically had probably on the order of 10--50 active participants tops (and often fewer). That was enough for a number of comments from each, and threads rarely hit the cap (though occasionally did). The end result read far more like a transcript of a real-life conversation than, say, HN or Reddit threads (or Usenet back in the day).
Again, HN tends not to produce such interactions, though they occur occasionally. Reddit is even worse for this --- it's where conversations go to die.