I like the way Reddit does this -- when someone replies to a comment you made, your mailbox icon at the top right glows red.

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).

This would be nice. I'd like to suggest a few things too. Sometimes I find good threads or interesting submissions that I want to read/analyze in the future, mainly because I don't have time at the moment, so I upvote threads. My saved list keeps growing even though I have done dealing in some of them. it would be great if you can delete it from saved list.

It'd be nice to be able to easily follow your favorite commenters as well.

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

You might also consider:

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.

Let me see a page showing the most recent comments on every thread that I upvoted, commented on, or voted on the comments of.

I might be thinking of a different feature but I like how on LtU it says "13 comments | 5 new comments" for example

My random thoughts on a way to keep track of this:

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.

I would like the option to get a summery email every 12 to 24 hours that shows which of my comments where responded to. I know you can look through your personal comments, but it's easy to miss someones response and after a few days it seems silly to send a detailed answer which is unlikely to be read.

What about an option on the threads page to order your comments by how recently they've had a reply (by any descendant comment) + associated RSS feed.

I usually prefer RSS feeds over emails.

Agreed, since RSS feeds can be emailed to you. It's more flexible.

Perhaps let users bookmark comment threads, and see what changes have been made by highlighting them a little, or putting a red star next to them?

You could tie that to upvoting just like for stories.

Perhaps some sort of interaction history that shows the last few threads you commented in if they've had any responses.

Just enable notifications by email. So an email notification when someone replies to my comment or to a thread.