Continuing the discussion from Suggestions for forum tweaks:
Discourse can’t be made fully threaded. If you simply select text you are replying to, it automatically offers the option to quote that specific text, as I’m demonstrating here.
You can also reply to specific comments rather than to the topic in general. When you do, your new comment is still just put at the bottom but you can see an indication that it was a reply to the specific earlier comment. And at the earlier comment it has an option to expand and directly show the reply.
The best way to manage tangents that threaded exchanges tend to have is to choose “reply as linked topic” and start new topics when going off on tangents. That option is by clicking the little arrow thing above the compose field. I’m going to do it now so that this reply itself is a new topic (since this is not a suggestion for forum tweaks).