One thing that people who compile these lists never seem to take into account is that the flagged discussions are only interesting to the extent that HN remains an interesting community, and that would not be the case if the site weren't moderated and users didn't flag off-topic submissions and flamewars.

The better HN does at fulfilling its mandate, the higher-quality the audience becomes, and the more people want to use it for other things (usually a marketing agenda or a political/ideological agenda). Often these people complain that the site isn't available to them for these purposes and demand that the filtration system be dismantled (censorship! suppression!). But if the filtration system didn't exist, HN wouldn't be a desirable target in the first place. It would in fact suck, because the best users—who come here to avoid getting barraged by marketing and political/ideological agendas—would have left. In other words, if you understand the dynamics correctly then these arguments refute themselves.