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Gonpachi, otherwise known as the 'Kill Bill Restaurant' located in the heart of Roppongi is one of Japan's best tourist hotspots for any movie fanatic.
Nonbei Yokocho, or Drunkard's Alley, is a tiny pathway spitting distance from Shibuya Crossing jammed with tiny bars, restaurants and izakayas. It's like a pocket version of Old Tokyo, and somehow still remains relatively hidden and unknown despite its sensational location.
Torikizoku serves cheap and tasty yakitori in downtown Shinjuku, Tokyo. 
Matsuya is a "fast food" chain that specializes in gyudon (beef and rice bowls) and curry, and is an excellent quick, cheap and easy place for a meal for travelers.
Vegetarian ramen seller in a busy restaurant in Tokyo station
The Milky Way Café in Tokyo is a star-themed cafe serving delicious ice-cream. It has a wonderful view of Ikebukuro and is the perfect place to relax when you need a break from traveling. 
Kimuraya bakery in Ginza is the birthplace of anpan and reportedly the oldest and first Western style bakery in Japan. The original sakadane anpan recipe includes sake yeast instead of traditional yeast, making for a unique aroma and delicious taste to the buns. The Sakura anpan includes a salted cherry blossom and is the original version requested by and presented to the Emperor Meiji in 1875. In addition, there are assorted varieties of kashi pan (filled breads) that include fillings such as curry, sesame, chestnut paste, cream cheese, brown sugar or strawberry. There are also cakes, loaves of bread and sandwiches including tonkatsu (breaded, deep-fried pork cutlet). The constant business of the bakery is a testament to the quality and heritage of this baking institution.
Sushi Iwa is a Michelin-starred sushi establishment located in Ginza, Tokyo, Japan. Master Chef Hisayoshi Iwa and Chef Shigeyuki Tsunoda really have a way with preparation, technique, and their warm hospitality. Best sushi experience for my guests from California and me!