I may be thinking about this all wrong, but for me anyway, when I see a fairly low-quality question / answer asked by a user with a reputation of 1, I am hesitant to downvote it. See the two most recent answers on this question. The reason I am hesitant to downvote is because it will have absolutely no effect on the user, while I will lose reputation. (Yes, I know it's not much, but it's something :). I am guessing that the reason for this reputation loss is to discourage excessive downvoting? My question is, though, if the person who I am downvoting is not losing any reputation, should I be? Could we maybe not lose reputation on those downvotes, since it seems that many of those answers are by users who create a profile for one-time use, and then go on their merry way? It seems to me it would be a way to signal to future visitors that the post is low-quality, while not losing reputation for downvoting someone who doesn't even care that they're downvoted.
I'd say it would be bad to promote the downvoting on answers from new users. They're new, and might not understand how Stack Exchange works. In this situations a comment can work wonders to help guide them. Down-voting isn't wasted though, as the system works out if someone repeatedly posts poorly received posts, and adjusts their ability to post if required.
Whilst on the subject of voting, I find it unusual how many questions have more answers than upvotes - in my mind, if a question is worth answering, it's obviously well written and useful, and deserving an upvote, surely?