Doesn't solve the question of following whole threads, but it's great for dialogue (not just because I notice when people reply to me, but because other people notice when I reply to them).

Edit: You can do this with Backtype, but a feature built in to HN would be great.

Let the server remember when a user has last opened a thread. If it is re-opened by the user, show only (or emphasize) postings with a newer timestamp.

1. RSS feeds where the link goes to the hn thread instead of the linked page? Though not everyone uses an RSS program integrated with their browser and opening an external program to keep track of HN threads isn't exactly good UX.

2. Keep track of how many comments were made when someone first views the thread and if there's any new comments, change the link color back to black instead of the grey that would show that it was already viewed.

3. The star icon previously mentioned. Have items automatically decay from the list after a certain amount of time (or time without a comment) to keep it clean. Upvotes can/should double as favorites since hn keeps track what someone voted for already.