GMail is really so cool. I think rather than just relying on quotation marks (> and such), it strips them and then diffs the message to its predecessors to find common chunks. I saw that in action when I sent an updated patch to a mailing list. In both versions, there were no quotation marks, but the second message, viewed in GMail, showed just what had changed versus the first message, the rest being hidden behind "--Show quoted text--" markers.
While nothing major, managing threaded conversations in chat has bothered me for quite a while. Yesterday I had an idea on how to improve matters: Works using existing chat infrastructure. Needs only augmented clients. Plays well even if other party uses a non-thread aware chat tool. Separates threads automatically based on interaction patterns. I've written an article and have created an online demo about it. Discussion welcome.