The Japanese are very fond of children, which makes traveling in Japan with kids a delight. All social reserve seems to be waived for children. Taking along some small and easy-to-carry gifts (such as colorful stickers) for your kids to give to other children is a great icebreaker.
Safety also makes Japan a good destination for families. Still, plan your itinerary with care. To avoid crowds, visit tourist sights on weekdays. Never travel on city transportation during rush hour or on trains during popular public holidays. And remember that with all the stairways and crowded sidewalks, strollers are less practical than baby backpacks. Many of Tokyo's major hotels provide babysitting services, although they are prohibitively expensive. Expect to fork over a minimum of ¥5,000 for 2 hours of babysitting.
Children 6 to 11 years old are generally charged half-price for everything from temple admission to train tickets, while children 5 and under are often admitted free. Tourist spots in Japan almost always have a table or counter with a stamp and inkpad so that visitors can commemorate their trip; you might wish to give your children a small notebook so that they can collect imprints of every attraction they visit.
If your child under 6 sleeps in the same bed with you, you generally won't have to pay for him or her in most ryokan (a Japanese-style inn), and some hotels don't charge extra for children. However, it's always advisable to ask in advance.
As for dining, most family-style restaurants, especially those in department stores, offer a special children's meal that often includes a small toy or souvenir. For those real emergencies, Western fast-food places, such as McDonald's and KFC, are everywhere in Tokyo.