If you go to the about page[1], you'll find extensions for both chrome and safari. These extensions will highlight new comments, as well as make comment threads collapsible (a la reddit).

http://hckrnews.com/about.html

These are great, but won't work on iPad, where I do most of my HNing. Server-side solutions are much preferred.

I really wish HN would adopt some of Reddit's features - ability to choose how comments are sorted for one, and the ability to collapse comment threads.

The browser extension found on the about page highlights new comments.