Oh god, please don't, at least not for chat/irc/whatever-you-call-it. I've seen so many attempts to try to somehow add another layer of order on top of chronological order. All the threads and whatever features and it is always a "what the heck is that, where are my messages, why did they get rearranged" disaster.
Like threads in e-mail, Usenet, forums on WWW?
IMO those are perfect examples of a combined logic and chronology. I'll speak for myself, but I absolutely prefer threads in the mentioned examples. It makes the content better readable. For me, there's no question about that. Although that isn't any proof; it'd be best to have usability studies about it.
If you're referring to conversation view, then they're not as good as traditional threads since they don't handle keeping track of conversation between multiple people that may branch off into different topics.
It never tried to hide messages from you, the threads worked more like filters. Instead of finding the discussion you wanted you filtered out messages that weren't related to that discussion.