Hacker News: Mark All Read for Chrome
More About Hacker News: Mark All Read
The data about marked as read items is stored on your local browser and is shared between HN pages: If you mark an item as read on the "news" page and it later makes it into the home, you will see it as read in the home too.
You can also choose to follow the comments of a news item: If you do so, the item will appear (with a different color) in the home page even if it was marked as read. You can mark the comments as read, and read the number of unread comments in the home page.
Last but not least, you can collapse comment threads, and show the parent of a comment you're reading by hovering on the "show parent" link. This way following discussions with lots of comments becomes easier.