The overarching theme with tags is this: we don't want to silo content for people, because that's a recipe for people missing out on content ("Wait, there's a main section?"). But we also want to make it very easy to filter on what you want to see and don't want to see, ideally building the equivalent of a personalized rationalist RSS. (Remember how you could read a bunch of blogs and then also comment on them in Google Reader?)

I think the appropriate historical allusion here is to the Blog Planet aggregator and its lookalikes. Not that I'm proposing this as a technical solution, necessarily, but it's a user experience I remember fondly.