Reputation is a great judge of quality and for certain things, and absolutely awful for others. For things that take a great deal of base knowledge to properly evaluate, like cryptography, quantum physics, etc. relying on reputation is generally the best bet unless you've studied the topic for years. There is simply no way to objectively and properly evaluate them for a significant majority of people. On the other hand, on topics that are inherently subjective, or topics that most people understand and end up having conflicting, subjective viewpoints, reputation is an awful way to evaluate the quality of content.

Most of the time on HN, reputation only contributes to the problem. Comments and posts should be evaluated based on their content, not on the person posting them. Reputation only fans the flames of "groupthink", "the hive mind", or whatever you want to call the inevitable tribalism that exists in every sufficiently large community. Reputation has a way of turning subjective opinions into de facto truths, even on things that are unrelated to the source of the reputation, and how could you possibly have an dissenting opinion on the truth ? Giving a popular, well known, "reputable" name priority has a chilling effect on discussion, since going against them is a surefire way to catch some heat from the rest of the community. If reputation and the popularity of a name didn't affect people's views, celebrity endorsements wouldn't be a thing.

The best system I know of is the one 4chan has. Everyone is anonymous, previous comments have no influence on current ones, and the only thing there is to evaluate is the content of your post. Since posts are ranked by time, not by score, every post has an equal opportunity, and it's incredibly difficult to cheat. Obviously that system also has problems, and a lack of threading is annoying at best, but at least it doesn't suffer from stifling discussion and punishing anyone who dissents.

The ideal system would be one where users have a per-topic reputation score, and the poster's handle isn't shown. This way eg. an expert on crytography doesn't have any sway in a discussion about marketing. The fact that someone is revered for their knowledge of networking says about the validity of their thoughts on economical issues, and should have no weight in those discussions. However I imagine this would be incredibly difficult to actually implement in a reasonable way, and could probably still be gamed, though it would be better than what we currently have.

Side Note: I didn't (and can't) downvote you, and I'm not sure why people feel your comment doesn't deserve to be seen.