I don't care for the NYT's editorial stances or reporting for the most part, but they've really been pushing the envelope in terms of using the newspaper's website as more than a paperless version of a dead-tree product. I could point to any number of their news-related projects. The election had a number of great ways to present election results. Their Faces of the Dead feature was also... how to avoid breaking the etiquette here... I'm going to go with "technically well-executed".