The Ghibli Museum in Tokyo is great if you're familiar with their movies.
There's also places called Round 1. Big sports and video game parlours. Pretty sure I remember seeing one in Osaka. You pay for a certain amount of hours. Not too expensive...just don't go overtime! And it's fun for adults too!! about 7 years ago
In Osaka theres a cool aquarium and a large IMAX theater next to it that has some cool documentaries. The theatre offers a discount if you buy tickets for both.
There's a ramen museum that lets you make your own cup noodles. You can buy a plain cut and decorate it, then choose 5 ingredients, they'll put them in the cup and shrink wrap it and provide a carry bag. That's at Ikeda, just north of Osaka. You can also make chicken ramen but I haven't done that yet.
For a day trip, I like tennoji zoo, and spa world. The zoos not the best but good for kids, after head over to spa world. They have amusement games, and 2 themed floors of spas, one for men and the other for women. The top floor is a water park for everyone so bathing suits are required there. about 7 years ago