The NYTimes example is by Khoi Vinh (http://www.subtraction.com/). He's certainly no design slouch, particularly when it comes to grid based layouts.

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.