NYTimes is an enormously complex site. Given the ridiculous number of priorities they have to juggle, and number of people they have to please, I think they do an admirable job. The site has to balance looking like a historic newspaper with the constraints of the web.
I particularly like Vinh and Boulton's presentation "Grids are Good" http://www.lifeclever.com/khoi-vinh-mark-boulton-grids-are-g... which applies a grid layout to a Yahoo type homepage.
See, that's certainly what they're trying to do, but I have absolutely no idea why they think "look like a newspaper" is one of their key constraints. You're a website: look like a website. The reason people don't read newspapers anymore is because they're inconvenient, why on earth would try to emulate a dying format?
Some people here love the NYTimes version but I really think it devotes a ton of space to features nobody really uses in an effort to force people to use them more -- something the NYTimes itself does. Of course, I hate the design of NYTimes.com itself, so maybe I'm biased.
SimpleScott's design simply reinforces existing usage patterns, and for that reason I like it best.