I really thought the Tsukiji Fish Market was awesome. Get there early!
Nikko is also amazing, loved it there.
Food is great, everything from Sushi to the ramen/udon/soba stands in the streets.
Itsakaya is cool too.
If your into the tech/gaming/anime culture, Akihabara is a must.
Shibuya crossing is cool to see as well, so many people.
Don't know if Tokyo has many, but try a night at a ryokan (traditional hotel/hot springs), was a really cool experience.
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