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.

Ars Technica's comment threads are mostly useless due to lack of threading and peer moderation.