I really like the way Twitter brings the context. I think inherently, many conversations are threaded. The problem tends to be how that threading is represented in the UI. Like Atwood, I like the flat structure. But I would love to see comments here (for example) have a small "in reply to:" link associated with it. So I could reply to a specific comment, have my reply still show up at the bottom of the list of comments (as it does today), but also carry with it a means to understand the context if you so choose. I feel like that gives you the best of both worlds.

Hey Jeff, GitHub's interested. I sent you an email with an introduction to our Head Markdown Guru. Let's make it happen!

Congrats Jeff! Having a daughter is yet different from having a son and you'll have twice that experience! Though now you'll have to transition from man to man defense to learn a zone defense as you're outnumbered. :)