I use this extension on Chrome, both marks new comments with a vertical orange stripe, and adds expand and collapse thread widgets, including one to collapse the whole thread you're in in the middle of: https://chrome.google.com/webstore/detail/hckr-news/mnlaodle...
Just to clarify: Do you mean there should be a refresh button for the comments view or should the app memorize what comments were already there the last time you viewed the page and highlight new comments?