I have never liked the threaded model, largely for the reasons pointed out in the link. Threaded discussion is nice when you first read something, but becomes a total pain in the ass instantly afterwards if you want to participate in the discussion and/or actively follow it (oh hey, there were 85 comments in the last refresh. Now there's 89. Time to go comment hunting, since they could be literally anywhere!). One of the most annoying cases I've seen is Techdirt - it offers both flat and threaded view, but everyone seems to assume that everyone is using the threaded view and doesn't properly quote the posts they are replying to, which essentially makes the flat view completely useless for trying to follow the discussion. And in threaded view, you can end up with ridiculously thin posts where they're practically unreadable. Oh dear.

This is why a strong quote system is absolutely essential for a great flat discussion model. I personally consider 4chan (powered with an userscript like 4chan X or with the inline extension introduced a while back) to be a fantastic example of this. With simple quote links, backlinks to replies, hover previews and inline quote expansion, you can follow discussion within a thread incredibly easily and even do basically on-demand threading! Allow me to demonstrate it with this image: http://i.imgbox.com/adss6lfu.png (functionality and style in this case provided by 4chan X[1] and OneeChan[2] with a slightly customized Photon theme)

[1] http://mayhemydg.github.com/4chan-x/

[2] http://seaweedchan.github.com/OneeChan/

Also, in regards to HN, a while back I thought about writing a userscript to turn the comment view to flat (with some sort of auto-quote links), but turns out it's not really possible because there's no way to get the accurate post times for comments due to the "X minutes/hours/days ago" - though this could be easily solved if the relative timestamp was wrapped in a <time> element (or heck, even a <span> with the accurate timestamp in a title attribute or something, anything).