Travelling in Japan is relatively hassle-free and the people are generally friendly, welcoming and helpful. Risk of violence and theft is low. The following are some basic tips and things you should be conscious of when visiting Japan.

Long-distance travel in Japan is extremely expensive, so if you intend on moving around a fair bit, you might want to investigate a Japan Rail pass.
When entering a Japanese home or restaurant, it is customary to remove shoes, and bowing is the usual polite greeting. Try to remember this at all times, but particularly when entering temples.
While eating a meal, it is considered bad manners to pour your own drink – you pour your companion’s drink and vice-versa.
Use chopsticks for Japanese food and regular utensils for Western food. Do not point your chopsticks at anybody, leave them pointing upwards out of your bowl, or use the same end that you have been eating with to dish up food for someone else.
It is considered bad manners to eat or drink while walking down the street.
Blowing your nose is also regarded as impolite
Tipping is not customary in Japan, and most people appreciate a gift more than money as a token of gratitude.
Try to learn and use some basic Japanese greetings and formalities, such as ‘thank you’ (arigato), ‘good morning’ (ohiyo), ‘good day’ (konnichi wa) and ‘goodbye’ (sayonara). It is customary to say ‘itadakimasu’ before eating and ‘gochisosama deshita’ after eating, especially if you're being hosted or entertained, as well as ‘kanpai’ for ‘cheers’.
Useful travel tips resources
Footprint Guides - Japan
Incomparable resource on Japan travel from this well-known travel guide publisher.
http://www.footprintguides.com/
Iexplore
Travel site with tips on ‘do’s and don’ts’ for a wide selection of places.
http://fodors.iexplore.com/dmap/Japan/Do's+and+Don'ts
Geocities
Excellent travel tips resource.
http://www.geocities.com/japanfaq/FAQ-Manners.html
More topics on this site…
Japan travel information
Japan health and safety
Japan maps and geography
Essentials
Visas: All US citizens, and most EU citizens, Australians and New Zealanders do not need visas for stays of less than 90 days
Season: March - May; September - November
Money: Yen
Language: Japanese
Emergency #: Tokyo English Life Line (TELL) - 3403 7106; Japan Helpline - 0120 461 997. (operator service)