This is a great idea.
This site is already radically different from other online communities, why not go full-bore and just make it based purely on a the-cream-rises-to-the-top model?
I would imagine the flag feature is enough to get rid of the spam or junk topics. If someone really likes a topic or wants to see it stay on the front page, they can burn up karma with upvote boosts (to a limit).
It seems the focus here is already on the community finding and upvoting topics of intellectual value and fostering stimulating discussion. Why not just bring that to a laser-like focus and drop all efforts at "punishing" or otherwise disciplining members of the community.
There's a big difference in motivation between thinking "what can I add to the discussion that will be appreciated and upvoted" versus "gee I sure hope I don't get penalized for saying this"... and that thought loop feeds back into the culture of the site. Right now I would (subjectively) say that 85-90% of the effort people put into the site is positive, while maybe 10-15% of it is negative (downvoting, indulging in a bit of flaming, etc.). If the architecture of the site was further refined to reduce channels for negative action, it would seem that positive effort component could get upped to 90-95% and make this place even more of a standout than it already is. HN could be one big proof-of-concept that a large, diverse, open community on the web can still be a highly evolved and civil community.
Dissenting opinion (from someone who generally believes in positive reinforcement as the best policy): I tend to be a very controversial figure, wherever I go. I have dropped out of a lot of communities in part due to the degree to which I get attacked. Some of my comments here get upvoted, downvoted, upvoted, downvoted. It can be entertaining to watch it. It usually doesn't result in some pissing contest. I am content with having people who don't like me/my opinions vent their spleen by viciously giving an entire downvote to my comment and then moving on. I'm very cool with that. It beats the hell out of anything else I've known so far.
[1] http://news.ycombinator.com/item?id=3116043 [2] http://news.ycombinator.com/item?id=3125017
I have a serious medical condition that is supposed to be killing me, and I do still have bad days at times, but I'm getting well when doctor's (and everyone else) says that can't be done (getting well is why I have slimmed down so much). To me, that is an ordinary fact and I talk about it casually at times online, the way I would to the two sons who live with me and know all the details. For other people, that's a headfuck and most folks divide up between being highly impressed or spitting in my face and accusing me of both making up crap and being a danger to others to talk about it (which makes me want to go "Okay, which is it? You can't have it both ways.").
In short, I guess I'm the anti-group-think wherever I go. AKA lightening rod for controversy.