Comment tracking twist: personalized feeds
The Evil Empire implemented an interesting new comment tracking system based on the display name that you use to leave comments: personalized comment feeds (via KC Lemson). Your display name is used to build an aggregate feed of all comments on the same entries that you commented on.
It makes it more manageable to track your comments and following replies, by allowing you to subscribe to only one feed per site.
Some structure is lost though, as these feeds combine different threads on different topics. But you could imagine aggregators being smart about these comment feeds and link their items back to the original posts (using the <link> tag in the items of the feed).