Harpers.org was recently redesigned by Paul Ford of Ftrain.com. From Ford's peek inside the process, Semantic Web technology was used to allow the massive amount of content Harper's has to be utilized in many different ways.
I have my doubts about Semantic Web technology, but this is a great example of how one designer, who has control over the ontology, can make it work.
And oh yeah, Harpers' still has some of the best written words in the world.