Looking at some humongous threads recently and I was thinking about how so much information gets lost in them because of multiple conversations in the same thread / posts and how to identify the conversations. Then I realized the solution. Attach some type of tag / marker to a post to identify each conversation. You can identify parts of each conversation based upon the quotes within each post. If a post quotes 2 conversations, no problem, just give it 2 tags. Having a way to manually select / automatically identify which part of a post goes to which conversation would be great, especially if it highlighted the areas (think of a box around the quote / response w/ a diffused background).
If a post contains text that doesn't refer to any previous post (e.g. no quote that it's responding to), then it can be considered the start of a sub-conversation. Because of this, each post has the possibility to start its own sub-thread. Yeah, this could get messy, but I'm sure there's some O calculations out there to help, and if not, time to make one lol!
For the crazier, multi-conversation threads, you could expand out to a tree view that shows the posts and how they're connected (probably easiest to show by each node being a post # at first, and not the actual text). There's a couple of PHP plugins that can draw on the fly, but the diagrams wouldn't have to be anything than just a tree diagram.