Right, "Newest First" does sort by the age of the top-level comment in a thread. 

It'd be neat to combine a solution for this with the highlighting that lllll Alaska Jack mentioned *and* some kind of selective collapse/expand: maybe sorting by "Newest" would still sort by the age of the top-level comment, but expand only those threads that contained comments you haven't yet seen, *and* highlight the ones you hadn't yet seen. 

It's tricky, because we don't want to sort replies out of context when "Newest First" is selected! More ideas/suggestions are welcome, if you have them!