100 Yen Stores - Japan has their own version of the dollar store. You can find everything from toiletries to furniture at these wonderful stores. They are great for souvenir shopping or picking up something you forgot to pack. Most items only cost 100Yen!
Train Stations - Need a last minute souvenir or need to pick up a gift for a host at the last minute? Try a large train station! Places like Tokyo Station and Shinjuku Station offer many places to shop for small trinkets, boxed sweets, or even cosmetics and clothes.
Morning Markets - Find everything from local produce to handmade crafts direct from the producers! Because there is no middle man you can get great prices on unique items.
Shopping Streets/Districts - Some areas are well known for certain goods. For example the Kappabashi area of Tokyo is known for kitchen goods. In these areas you can find many competing shops which means great prices on specialty items!