If it's used to indicate a well thought out and structured point, then how do people convey agreement with that point?
If it's used to convey agreement, then how do we make sure that things that don't contribute to the conversation?
The same is true for downvoting. Downvoting becomes available above a certain karma threshold.
Abuse of either, i.e. using them in ways that are known to be detrimental to HN historically can result in various sanctions by the moderators (none of which are explicitly stated).
So vote something up if you think it should be voted up. It's that simple.
I think comment downvotes are supposed to be the opposite of the above, but in practice it seems to be used to say "I don't agree with you," or "you don't know what you're talking about."
Mere agreement or disagreement should probably be handled with a comment, to further the conversation. You could easily disagree with a comment, but upvote it, if you thought it contributed something worthwhile.
There are Guidelines and a FAQ at the bottom of most pages.
Pro tip: If you downvote comments you don't upvote, you get twice the voting power.
(^^ or really, don't do this, treat voting more as a pavlovian thing.)