There is a similar "karma" system on my social network, and one of my users suggested that we limit the amount of karma a user can receive within a give day. On YC, it makes sense to limit the submission volume according to the person's karma level. Someone with high karma is unlikely to be spamming the site.
This, combined with a burying system to get rid of junk stories, could clean up the 'new' section substantially. It would also be useful to factor snr into the computation; the nature of the karma system, which makes it more advantageous (at a marginal level) to submit a story than a comment, encourages a shot-gun approach to submission; SNR would combat that.
EDIT: Ha, points to jwecker for posting about SNR while I was writing about it.
I've never used Digg, but from what I read of them, their burying system is working out rather poorly. Burying a story on Digg requires an O(1) number of votes, so anything controversial gets buried even if 90% of users agree that it's an excellent article. A simple up/down model like Reddit's seems like a better idea, but see the top-level comment that I'll have posted in about two minutes.
Well, there's also signal-to-noise ratios. There are some people who have high karma by submitting dozens and dozens of sites knowing that one or two has got to stick. To me that degrades the quality of the site as much as spam does. I guess your solution might solve that in a round-about way as well.
I would abstain from complicating the user experience, though. In my experience, posting a topic has much more potential in gaining points than writing *thoughtful* comments. A good strategy to rise above that ranks is to post a bunch of interesting links; upon achieving high points, the user can then take a defensive stance by defending his or her opinions through posting comments instead.
The point is, from a user's perspective, there is more to gain from posting topics than comments.
That is certainly the status quo; I would ask, however, whether it is desirable. I think the system should provide more incentive for thoughtful comments, or at least some sort of disincentive for shotgun-style submissions. It is difficult to build karma by posting lots of comments; you have to put the effort into generating good content to get karma. The same should ideally be true for submissions; the difficulty, of course, is that since the content of submissions is generated by someone other than the submitter, simply posting lots of them /will/ eventually result in a karma-boosting hit.
We had a similar problem on our social network where users abstained from giving karma to thoughtful comments. Consequently, we coded an algo to add "+0.1 karma" to every user that gave another person "+1 karma". That was enough to take care of the problem.
