Nutritious Japanese snacks [a work in progress]
The Japanese diet is superior to the western diet in many ways and, although western snacks such as cookies, potato chips and other sweets are easy to find, low cal and nutrition dense foods are easy to find.
Let me define my terms here. Low cal are foods that are less than 150 kcal/serving. Nutrition dense are foods that are higher in calorie count, but have significant nutritional value, as opposed to the "empty calories" one often finds with sweetened and fried foods.
At almost any convenience store, you can frequently find a very small selection of fruit, usually bananas, lemons or oranges. The basement floor (B1) section of almost any large department store will have all the usual fruits and veggies you get back home.
This link from Japan Family Guide has a good rundown on grocery shopping in Tokyo: http://www.japanfamilyguide.com/shopping/74-grocery-shopping-in-tokyo-and-other-japanese-cities
If you want to get local with your healthy snacking, my top choices are:
1) Senbei, baked rice crackers, are higher in calorie count, but don't have the problems associated with fried foods.
2) Yogurt. Who can go wrong here? The variety you find in stores here tends to be spartan compared to their more flavorful (and sugar-laden) US cousins. If you're not used to it, plain yogurt will taste bitter and, well, awful. But, flavored with real fruit (bananas, strawberries, kiwifruit, etc.), and you have a true treat.