National Museum of Nature and Science, Tokyo

Took the two older children to the National Museum of Nature and Science, or Kahaku, in Ueno Park. If you haven't been I'd throughly recommend it as a good day out. Cheap also as adult entry is only 600 yen and children up to 18 get in free. (Mind you, the restaurant is a little on the pricey side, espcially as the menu consists of the Japanese attraction standard fare; curry rice, meat sauce spaghetti etc.)
The museum itself is split over two buildings. The older building or The Japan Pavillion, which in itself is worth the visit as old buildings are few and far between in Tokyo, houses mainly a collection animal and plant species native to Japan. Although at this present moment it is closed for refurbishment. The newer building, The Earth Pavillion, house dinosaurs (big with my children!) and six other floors of exhibits of showing the relationship between the earth and the creatures upon it. My children enjoyed looking for the animals in the third floor Woodland Wonder and playing with experiments on the second floor.
If you visit and it's not raining take your kids up to the roof where you'll find about half a dozen giant parasols that open and close when triggered by movement sensors.

But the really great thing about the National Museum of Nature and Science are the multi-lingual explanations. Next to each exhibit are touch screens that explain what it is you're looking at. A simple touch switches the language to English, Chinese or Korean. The museum also rents an IC card device that you carry around and touch against the explanation stations, when you return your IC card you take the paper card from the device and using the log in and password provided can access the explanations again at home over the internet. Great if you have impatient kids, like mine! Be sure to ask for an IC card at the desk just after you enter the museum.