We just took our toddler to Tokyo in May for the second time. She loved it (in fact she had been begging to go back for an entire year). We stayed in Shinjuku. Here are some things that she enjoyed:

• We purchased the video Big Bird goes to Tokyo and loaded it on our ipod video before the trip. It was a big hit and we saw many of the sites from the movie when were in Japan. The Park that big bird goes to when he gets lost is in Shinjuku about two blocks from the hilton. Our daughter enjoyed seeing it, but there were a lot of homeless- so not the kind of place I would just let her run around.
• We went to the Kiddyland toy store- you can find directions on line. It was a hit.
• We went to Sanrio Puroland. An AWESOME day trip with a toddler. Everything is suited to kids their age. Go on a school day, not a weekend.
• We took a daytrip to Fuji and Hakone and returned on the bullet train- also a big hit. There is a lot of sitting on a bus, so plan ahead with activities.
• Took a morning tour of Tokyo. Typical Japanese tour- on the bus, then off for a short time then on again. Perfect for a toddler's short attention plan
• We stayed in Narita for one nignt on each end of the trip and took the shuttle from the Hilton to the Mall. The mall has an indoor playground which was fun, but there is a department store with a huge indoor supervised play area (costs about $5 for 1/2 hour) which she absolutely loved. She STILL talks about it.
• We didn't hit Disneyland on this trip because we already had a full schedule, however, be aware that entrance is actually substantially cheaper in Japan than in the U.S. Toddlers are Free : )
• It is much easier to get around Tokyo for non Japanese speakers than it used to be. There is a lot of signage in English now and the train stations usually have people who will help you. The Japanese also are very friendly and enjoy children. I recommend that you always carry a card with the phone number and address for your hotel in Japanese, so you can show it to someone if you get lost.

Strollers work pretty well in Tokyo, but there are still train stations where we were not able to find ANY elevators. So, bring something that you can carry along with holding the toddlers hand.

We did the trip in diapers one time and just potty trained the other. I was able to find appropriate facilities each time. My daughter will eat pretty much anything, so we didn't have any problems. McDonalds are all over the place in a pinch.