Top-level comments should introduce arguments; responses should be responses to those arguments.
Upvote and downvote based on whether or not you find an argument convincing in the context in which it was raised. This means if it's a good argument against the argument it is responding to, not whether or not there's a good/obvious counterargument to it; if you have a good counterargument, raise it. If it's a convincing argument, and the counterargument is also convincing, upvote both. If both arguments are unconvincing, downvote both.
A single argument per comment would be ideal; as MixedNuts points out here, it's otherwise hard to distinguish between one good and one bad argument, which makes the upvoting/downvoting difficult to evaluate.
In general try to avoid color politics; try to discuss political issues, rather than political parties, wherever possible.
As Multiheaded added, "Personal is Political" stuff like gender relations, etc also may belong here.
Incidentally, my biggest problem with these threads comes from the fact that the positions I'm most interested in hearing good arguments in opposition to, I suspect I wouldn't find any opposition on here. I'm fairly aware of the first-principles differences which result in most of my disagreements; the baffling ones are things like support of drone warfare coming from people who believe in universal healthcare. (I can see support of one, or the other, but not both at the same time. And yet people exist who do support both at the same time.)
2OrphanWilde
Fair enough, but they do seem pretty civil thus far. I've been monitoring them to make sure they don't get out of hand, and that they don't start infecting the rest of the discussions. (There have been a couple of political-leaning topics, but no more than before, and I think maybe less.)
As Multiheaded added, "Personal is Political" stuff like gender relations, etc also may belong here.