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Hinohara-mura(village), Nishitama District, Tokyo
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ditto
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haha-jima(Island),Ogasawara-mura(village), Tokyo
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Mitake, Ome-shi(city), Tokyo
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Okutama-machi(town), Nishitama District, Tokyo
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chichi-jima(Island),Ogasawara-mura(village), Tokyo

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Please keep suggesting places, please! :)

In Ueno you can enjoy in a Japanese tradtional style restaurant "Nabemono" such as "sansai Kamameshi". My favourite is "Kani Kamameshi". Tamago was warm. Suhsi and Tempura and other food were fresh and delicious. A Japanese friend from Tokyo led me to this local people restaurant. The responsible is a very kind Japanese woman (she's like a lovely mother) who is caring a lot for her guests. She corrected my Japanese and she's very funny. (See address pictures as I still can't read lot of Kanji).

My Japanese friend is born in Kanda. So, i recommend you to take a walk in this districts with its interesting shops and café. I would say it's like a kind of soho quarter with some old shops.

If you are interested in art, I recommend you to visit during a late afternoon different galleries in Ginza. You will see good paintings and sculptures and you will have nice talks to interesting artists.

Have you ever tried a capsule hotel ?

Have a look here :
Tweety's peregrinations in Tokyo

If you are visiting Asakusa and the Sensoji, you have to take walk to the new Tokyo Skytree. Just look for the tallest tower you have ever seen, and walk toward it, it takes only 20 minutes or so to get there.

If you visit the fish market in Tsukiji (as many visitors do), you should visit Tsukishima. Cross the Kachidoki Bridge (the old metal drawbridge), and turn left at the first light on the other side. Follow the road straight, and it will lead you through an old-style Japanese main street. Tsukishima is famous for it's old-fashioned shops and stores, and for it's numerous Monja-yaki restaurants.

Another place to see is Tokyo Cathedral, which is fantastic Catholic Church designed by famous Japanese architect. After visiting the cathedral, visit the garden at the nearby Four Seasons Chin-zan-so hotel. This is one of the most beautiful gardens I have seen in Tokyo, and you don't have to be a hotel guest to have a look. There are some nice traditional restaurants located on the grounds of the garden, and they are as nice to eat in as they are to look at.

Thanks for the post! This is exactly the kind of stuff I'm talking about.

I would definitely go to Shibuya and go to see the crossing there if you havent already. The Starbucks across the street from the station has a great view from the second story of all the people walking across. If you are more into temples and whatnot I would go down to Kamakura, it is a little far down to the south though. Harajuku is always interesting just to see the fashion of the people who shop there.

Coming out of the Yotsuya station there is a tiny street to the right of Shinjuku Dori that is full of hole in the wall bars and restaurants. I studied at the university at the station and explored quite a few of them. The Japanese who go there were always up for conversation too.

I'll add to seeing Shibuya for the scramble cross walk and the bus terminal.







There's some very impressive buildings in the fashion district

Odaiba!
 

Have you considered Odaiba?
You can experience new and old Tokyo.
This may help:
Visit Japan 2011 (Japan travel UPDATEs) | Facebook

Everyone goes to Shibuya and Harajuku. Personally, I feel uncomfortable when I am surrounded by foreign tourists, I like to go to places off the beaten path. I often go on long hikes or bike rides in different directions with no destination in mind, just to see what I might come across.

If you want a bike, you can buy one for next to nothing on Craigslist Tokyo, or you can rent one at the Oryx car rental shop near the Yaesu exit to Tokyo Station.

Starting with the Imperial Palace in the center, you can ride to many different places. You can take the road from the Sakura exit from the palace, and follow it all the way to Tokyo Tower. There are numerous shops, shrines, and other places to see along the way.

The next street is Roppongi Dori, which will take you through Akasaka (near the US Embassy), to Roppongi, and then on to Shibuya. On this road you'll pass Roppongi Crossing, and pass by Roppongi hills. You can follow the signs to Aoyama Cemetery (worth seeing, and seldom visited by tourists). After passing through Roppongi, the road will eventually take you to Shibuya.

The next road leaves by the Hanzomon gate, and this road leads to Shinjuku. Along the way you'll pass by Yotsuya, and you'll see Yoyogi park on your left. Bear to the right before the tunnel to get to Shinjuku. You'll pass through the ni-chome area, which is Tokyo's so-called "gay" district, and then on to Shinjuku Station, crossing near the east exit.

To the other side of the palace you can go to Yasukuni shrine, which is dedicated to the Japanese soldiers who died in the war. This area is also near Kudanshita, where the Japan Budokan is located.

If you leave the Yaesu side of Tokyo station, and go up Yaesu Dori to the third traffic light, you'll find Chuo-dori, this will take you through Nihonbashi and Kanda. In Kanda there are many small streets and alleyways with many interesting food shops and stores. Past Kanda, you'll run into Akihabara. Akihabara is quite overrun with tourists nowadays, and the shops are more expensive than you'll likely find in your own country, but it is a fun enough place to visit.

After passing through Kanda, you'll go through Okachimachi and come to Ueno. If you go off to your right, you'll come to Ameyoko, which is the discount shopping district which has been a busy place since the end of the war. After visiting Ueno, you can find Asakusa Dori on the other side of Ueno station. You can follow this road to Asakusa, and places beyond, such as the Tokyo Sky tree, Kinshicho, and eventually Kasai or Urayasu.

Tokyo is not a difficult city to find your way around, if you become irretrievably lost, you can always hop into a cab and have them take you to a familiar station or landmark.