The entire up vote/down vote thing needs to go away. Voting on a story should be related to an action that the user is taking which implies an up/down vote.
For example, in my Facebook application Wildfire stories are up voted only if you pass then on to your friends. As you mentioned to me yesterday, delicious/popular is interesting because it's based on pages people bookmarked for themselves.
I think the hardest part is finding what behavior to track. Click-through is obviously bad. Bookmarking and passing to friends will also slant the stories in a way that isn't necessarily good. I have a lot of friends that don't really care about hacker news, and tend to bookmark more reference-type material.
Comments are useful, but that slants towards controversial topics.
Simple idea someone might want to found something on: provide a little highlighter extension for browsers/in a wraparound frame/as a bookmarklet. Track pages people highlight; title and describe them as the few most highlighted words.
Not sure if I'm the exception to the rule, but I definitely highlight random crap while I read a page (just something for my mouse hand to do)... so I'd ruin your stats in a mean way.
The problem inevitably becomes what do you do once the community has become larger? How do you keep the topics and the level of discussion from sliding downward? This is an issue that Lambda the Ultimate's been facing for the last couple of years as less academic, more industry people join the community, and they've been handling it fairly well but it's taken a lot of work on everyone's part. Reddit's facing the same issue as well. If there are more dumb people than smart ones in a community, they can dictate what articles make it to the front page and overwhelm the good discussion with drivel.
For example, in my Facebook application Wildfire stories are up voted only if you pass then on to your friends. As you mentioned to me yesterday, delicious/popular is interesting because it's based on pages people bookmarked for themselves.
John.