Good luck getting into this "secret wine bar" that everybody knows about; they don't take reservations after 6:30pm, so be prepared to line up. Wines from the rotating list - mostly French, mostly biodynamique - start at Y800 a glass, while the food tends toward simple but well-prepared bistro fare along with fresh-baked bread. Budget around Y6000-8000 for dinner and drinks.
This book will introduce you to more than twenty of Japan's favorite specialty foods that are less well known abroad, along with a guide to the best places in Tokyo to try them and expert tips on what to order. From Bento.com.