If you think it's more worth reading than the average in that thread, vote it up. If you think it's less worth reading than the average in the thread, vote it down. If you want to conserve peoples' feelings, vote down less often than these instructions suggest.

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.)

There are many. For a collection of data points on how people tend to do it, look at this post.