Eleni's in NYC. Saw them on Food Network last year, and went to visit them last weekend. Beautiful cookies and cupcakes but not worth the calories. A better bet: Magnolia in NYC, Sprinkles in LA and Cupcake A La Mode in Kansas City. (Not that I'm an expert in this topic.)
Elinis was ok, but I was uber-impressed with Chelsea Market. One Lucky Duck (raw, vegan and organic, but mostly just tasty) and the Lobster Market - yum!