Here's the thing: I think threaded/collapsible/sorted comments are good for technical discussions, or for discussions which break apart into sub-conversations you want to be able to ignore. I know that's a very natural model for me, and for people accustomed to computing or other "hard" sciences.
But I know a lot of people in humanities, arts, or social sciences who hate threaded comments because they view a complex, interleaved conversation as the best result. I'm not sure they're wrong, either... I certainly have more trouble following those discussions, but they also seem much more broadly connected. And back-and-forth flame wars between individuals are (slightly) rarer.
In small or restricted communities, that can definitely be the case. But I've never seen a large community with good comments that didn't have some or all of the above features.
The one that comes to mind immediately is MetaFilter. Not huge, but a pretty decent-sized community and above-average comments. No threading or non-chronological sorting involved.
John Scalzi's blog Whatever also has a pretty large pool of commenters in a standard Wordpress setup.
The thing both of these have in common is active moderators.
But I know a lot of people in humanities, arts, or social sciences who hate threaded comments because they view a complex, interleaved conversation as the best result. I'm not sure they're wrong, either... I certainly have more trouble following those discussions, but they also seem much more broadly connected. And back-and-forth flame wars between individuals are (slightly) rarer.