1. Gender politics
2. NSA/surveillance
3. Vim/Emacs
And I could name at least 2-3 regular commenters on HN who fall pretty cleanly into each of the opposing sides of these issues (ok, maybe not Emacs, but all the others).
Just because we're not degenerating into flame wars doesn't mean we don't discuss divisive topics.
Those topics are poisonous because they can't be driven to a conclusion in two paragraphs or less. And most everything's been said, so they run in circles rehashing tired points. Not to say they aren't important topics. But it takes an essay of 100 pages to cover all the ground, or a PhD even. But everybody has opinions, often based on whatever they just were thinking about. Their arguments come off as sophomoric (which they mostly are). Folks point that out, and away they spin.
They are poison on voting sites because one side quickly becomes grey. Votes do nothing but squelch conversation, and many choose to self-censor to avoid that.
The most divisive thing you can do on HN is point out the obvious true fact that there's no such thing as a self-driving car yet.