I like the karma system overall, and I think the general quality of discussion on HN is evidence that things are mostly working well. The only thing I find off about it is the average karma on profile pages. Personally, I find that it subconsciously dissuades me from commenting anywhere that is likely to result in few/no upvotes. My first comment on a story might get 20, 40, 80 upvotes, but any extended discussion is…
It's not just commenting on unpopular articles and deeply nested discussions that will pull your average karma down, but commenting on old articles.
By the time I find an interesting article to comment on, it will usually be at least a day old. Nevertheless, I tend to comment there anyway, in full knowledge that very few people will ever read my comment or upvote it, because most of the action on HN happens within the first day, and most people move on to the newest articles very quickly.
The way HN handles average karma calculation in such circumstances is pretty sad because of the disincentive it places on people to comment on good older articles, which are often much more interesting and worthwhile than your typical new article.
This problem is compounded by HN's attempts to disallow duplicate article postings (though there are ways around that), and lack of automatic linking to previous discussions on the same article (though manual linking is occasionally done by HN users themselves).
In short, there should be a way to keep productive discussions going, rather than effectively placing a limit of about 1 day on any given discussion.
I hate to praise web forums in any way, but I do think one thing they get right is to usually bring any threads which have been recently commented on back to the top. HN would benefit from a similar approach.