There are no repercussions for upvoting or submitting questionable content at the moment. While my proposal is only a small penalty, hopefully it gets people to at least think before actions that potentially increase noise.
Edit: I meant "when a submission gets successfully* flagged", ie killed. Thanks davidw for pointing out the ambiguity.
This is a huge factor, IMHO - a much higher signal/noise ratio in the articles on the front page would probably set up positive feedback, helping with other issues. Unfortunately, there are positive incentives for being the first to submit anything that could potentially be voted up, drowning out interesting content.
One way around that would be that if a story is killed, then and only then does the penalty occur, and it's sharp.
I think it really comes down to a human solution to a human problem: tech only goes so far to fix problems like these.