When staying in Japan, perhaps the cheapest, and most characterful would be to stay in a Minshuku. Minshuku are the Japanese equivalent of a bed-and-breakfast. Minshuku represent pretty good value for money and are very Japanese though I’m not too sure how many there are in the centre of Tokyo. These, like Ryokyan, will have shared bathing facilities. In Tokyo, I’ve always enjoyed staying in the Park Hotel, which, starting on the 30th floor, offers some fantastic views the city, of Tokyo Tower, and of Mount Fuji.
If you’re planning to do any travelling outside of Tokyo, you’ll want to pick up a Japan Rail Pass which offers extremely cost-effective access to Japan’s comprehensive, but otherwise expensive, rail network. The rail pass comes with only one notable restriction: you won’t be able to use the Nozomi trains; the fastest of the Shinkansen.
Be sure to take the time to experience at least one Onsen.
Seasons; Autumn colours, etc.
- Tokyo Tower
- Tsukiji Fish Market
- Tokyo Skytree
- Ghibli Museum
- Gyoza Stadium, Ikebukuro
While in Tokyo, it’s also good to visit one or two of the parks. These typically cost to visit, but offer a fantastic escape from the city.
From here, you can walk to Shibuya.
Japanese ‘gothic’ hangout and good for amusement on a Sunday afternoon).
Odaiba is a man-made island–built entirely, I believe, from rubbish–and offers a the more kitsch Japanese experience. It plays host to a number of shopping areas, including Venus Fort, a shopping mall themed after an Italian town, complete with fountains and simulated sunsets.
There are some pretty great views from Odaiba, and, looking back across Tokyo Bay to the mainland, you can put the city in context a little better.
There are also some great views to be had from the free observation decks of the Tokyo Metropolitan Government Building, located in Shinjuku.
Outside of Tokyo, there are three popular locations close worthy of a visit (though you probably only want to do one of them): Nikko, Kamakura, and Hakone (the first two are essentially temple hot-spots and the latter just a pleasant location with a good view of Fuji-sama on a good day).
Nikko can be reached from Tokyo by train, with the last part of the journey on a funicular train that winds through the Japanese countryside.
Some sample of shrines, good train trip to get here.
nr. Tateyama - Museum of old houses
Round tour with boats, cable car, funicular railway. Might be good with young kids.
Giant Buddha. By the sea. Nice beach walk.
Be sure to check out Kanazawa Castle, and Kenroku-en.
Miyajima is an island just off the cost from Hiroshima. It’s somewhat of a journey from Tokyo, but is still relatively accessible by Shinkansen. If you’ve ever bought any Japanese guidebook, you’ve almost certainly seen a picture of the torii (gateway) of Itsukushima Shrine, set in the sand.
I’d recommend spending a night or two in a Ryokan. There seems to be a pretty comprehensive listing of accommodation available here.
If you’re heading West, Nagasaki is a very interesting place to visit and, being that it represents one of the first international ports in Japan, has an almost European character in some places.
Japan has a wealth of natural onsen, or hot springs. You can find them all over the country. This makes it hard to single out any one place to visit, but I’ve certainly enjoyed visiting the onsen around Lake Tazawa.
Japan Guide seems to have a pretty good listing of the various Onsen available in this area.
The ryokan and onsen here will expect to pick you up from a train or bus station and return you at the end of your stay. Once you’re there, you can simply enjoy the food, hot springs, and countryside.