Threaded comments—like here, on HN, and on Reddit—easily spiral out of control. It's especially hard to come back later and see what's new.
Many people seem to have missed this, but Discourse solves the problem in a particularly elegant way. Each topic is about, well, a single topic. The conversation flows as a series of replies, ordered chronologically.
If, however, you'd like to change the topic, there's a "Reply as New Topic" button to the right of every post. This allows you to create a new thread, with a new topic. Metadata about this forked topic is saved, so that future readers can easily bounce between related threads, while still having every message in sequence about the same "topic."
In my experience, this approach maintains the simplicity of flat discussion with the ability to fork topics of nested threads, without the complexity.