I would have liked to see Trier, Germany on this list.  It's a beautiful old, Roman city.  When I was there it wasn't popular with Americans.  My favorite places in Europe were off the American tourist radar :), at least when I was living there.  
In the States, one of the most beautiful places to visit is the Provincetown Dunes at sunset, near the end of Cape Cod.  
El Yunque, a rain forest in Puerto Rico, should have also been on the list.
The New York Times list, in some ways, is quite biased.  They missed out on some good stuff.