I have a browser plugin that highlights most recent unread comments on HN with a yellow background, and counts new comments in the thread listings. One could even add "next unread" links as well.

I've seen imageboards that toggle between a flat and tree view with javascript.

Any feature you can think of has probably been implemented by someone at some point. Unfortunately almost no one cares about forums anymore so trying to innovate in the space is a waste of time. Only a very fringe subset of nerds (myself included, I still weep for my HN clone in Hack that will never be finished, and my Godot client that will never be released) considers forum UI design to be interesting.