Here's the idea. Put a character beside each headline, something that doesn't otherwise have meaning like the tilde ~. Link it to a script that sets a cookie for the user indicating that the headline has been "marked as read". Headlines that have been marked as read would then show up in a strikethrough font, but only for that particular user. A reader that clicked a second time on the tilde would be marking that headline as unread thus reversing the initial action.
This sample from the comments here on Random Bytes illustrates best what I am referring too. Unfortunately, I don't have the skills to write the code that makes the tilde functional, so squint and pretend.
Doug Re: Congrats to Me ~
Arnold KlingRe: End to End and Top to Bottom~
Ross Re: Spam, Accordians & And - Docflocking Redux ~
MichaelRe: Spam, Accordians & And - Docflocking Redux~
Nothing simpler, neh? Of course, this should also extend to regular headlines and not just those of the comments...and the primitive should be consistent between as many tools as possible. This kind of stuff only works if users view it as predictable and familiar.