Do you pick a date for all users and anything before that which hasn't been explicitly saved rolls off? Or each week you find the oldest unread item for each user and set that as the "mark read" date for the category? I like the second, but I think you're talking about the first. The thing I don't like about that is that I could be away for a while, and when I come back I'd want to see the same state as when I left. (Plus new items of course.)
I'm not sure how my preference would affect the queries you're doing.
As to "formalizing" the articles, I'm thinking the same thing. But for it to be meaningful, I think you'd have to have some sort of restriction on who can post an article. Whether it's a user-filtered queue ala K5, editorial selection ala /., or list of approved editors ala IWE or other trade pubs. In one sense it's just another launch point, but there has to be some exclusivity to it or it's useless.
That's why I suggested three different types of main page. Right now we're a free-form site. Someone using this software for a site like The Register or LinuxToday would want something that sees the article as the main thing, but with richer discussion than they have now, and a place to put open content.