If you allow comments? Thread them.
Period.
I don't care if it's more work. I don't care if it doesn't play nicely with your infrastructure. When people are saying things, they're usually saying them in response to something else that has been said, and making it easy to see how these things line up with one another is essential to the actual "communication" part of that whole saying stuff thing you're enabling. Otherwise it's all just half a cell-phone conversation in public, which is both useless and annoying.
Comments are threaded. ALWAYS.
I have decreed it! Now make it so!
