Why I organize comments on WanderingThoughts the way I do
DWiki has a pretty simple way of displaying comments; all comments on a single page, which also has the main entry. There's a lot of more sophisticated comment handling systems, like LiveJournal and Slashdot, and I won't deny that part of why DWiki is simple is that simple is less code. But part of it is deliberate, because it's all about the context.
Specifically, I want people who read comments to have as much context as possible, which means that I want them to at least have the chance to see all of the comments along with the original entry. I prefer flat comments over threaded comments for the same reason; flat comments force a theoretical reader to at least skim the whole thing, instead of narrowing in on just one aspect of a discussion.
(This is true of threaded comments even if everything is displayed on the same page; people are good at quickly skimming visual structures.)
The other advantage of flat comments is that they push things towards staying as a single conversation, instead of multiple conversations diverging down each different thread. Well, assuming that one squelches heated side exchanges somehow, before they take over the entire conversation.
(I believe I got this cluster of ideas from Joel Spolsky, although he wasn't writing about blog comments.)