This is my favourite - adds a lot of nice stuff, and though it sometimes breaks due to site changes, it's always updated pretty quickly to fix issues. And it's open source: https://github.com/etcet/HNES
highlights lines beginning with ">", which helps differentiating quoted replies from comment text. And yes, the idea comes from imageboards, but a lot of people on HN use that syntax in their comments.
On Safari I use hckr news[0]. It highlights new comments in threads I've already visited, and allows collapsing. There is also the option use the homepage there, but I just use the normal one.
Hacker News Room http://hackernewsroom.com is a web-based HN reader, built on the official HN API. It's not a browser extension, but it has some nice features including folding comments. And it works well in all modern browsers.
