In general, I try to upvote if I think the author made a good new point in the discussion (or made an old point in a better way). I also vote up humorous comments if I find them funny and if they don't detract from the surrounding conversation.

I try to reserve downvotes for occasions where the author is not just espousing a conclusion that I think wrong, but when they are making a rationalist mistake in the particular comment:

• when I think they're ignoring or misunderstanding a valid objection, or completely missing a particularly obvious objection
• when I think their bad writing style obfuscates rather than clarifies their content
• when I think they're behaving badly towards others or established LW norms of conduct.

On the subject, newcomers should be aware that there's some karma-based limit on how many downvotes you can make (to prevent trolls from mass-downvoting everyone they disagree with, etc), but I think it's rare to hit that limit.

EDIT: By the way, welcome to Less Wrong! Check out the welcome thread if you haven't already. (One point it doesn't make: unlike most blogs, you can comment on older posts and still get a conversation, because many of us regularly follow the comments feed.)