Heres my contribution, (refers to Tokyo mainly, By the way I did not write this up, found it) :
One of the best guides to all thing Japan is Japan-Guide which has a lot of good and useful information. The forums here are a good place to research topics that aren’t covered in other sites.
Japan Travel Guide: Essentials
Top Hot Spots in Japan –
Welcome to Bento.com - For reviews on all the best places to eat in Tokyo, Kyoto and Osaka.
Featured Topic: Tokyo Hip Cities | MustLoveJapan - Video Travel Guide of Japan - For information on the top hot trendy spots in Tokyo
Virtual Guide -
If you are interested in a virtual tour of some of the major tourist spots you can go to the following website which gives you a street-level 360 panoramic view of the city.
Travel to Tokyo now - Panoramic Photography and Map - 360 Cities
Volunteer Tour Guides –
TokyoFreeGuide has a service where local university students and/or ex-pat foreign nationals are available to help guide you through Tokyo and specific areas. Most speak Japanese and English fluently and can also act as translators. Tips are not required but parties may need to pay for food, travel and other admission fees associated with the guided tours. They do need up to three weeks advance notice of the trip. -
TOKYO FREE GUIDE - Volunteer Tour Guide Service in Tokyo
An article about their service was featured here:
Tokyo Tour Guide – For Free! | Travel Happy
Expenses/Costs -
Tokyo is one of the most expensive cities in the world (rivaling New York and London in general product costs). Research prices of everyday items and services before you go to get an idea of how much you are going to be paying for items. One site that might be useful is PriceCheckTokyo which you can use as a guide. Please note however that this website may not reflect the most current costs of items in Japan:
http://www.pricechecktokyo.com/
Onsen Recommendations –
One of the best places to find information and recommendations on good “onsen” (Japanese Hot Spring) is
Onsen Japan -- Japanese Onsen reviews, Japan onsen photos, guided Japanese hot spring tours, spa recommendations, and more which has a fairly impressive listing of most of the major onsen in Japan as well as local favorites. Includes prices, photos and short descriptions of all the onsen covered.
Customs and Etiquette-
Just because you’re visiting from another country, don't expect the Japanese to be understanding of cultural faux pas. Get a head start at being familiar with Japanese customs and etiquette as this will impress those that you meet during your visit:
Etiquette in Japan - Wikipedia, the free encyclopedia
Public Transportation -
The JR and transit system can be so confusing so it is a good idea to be familiar with your travel options including JR and subway routes:
Travel Within Japan | Air | Train | Ferry | Bus | Taxi :: Japan Visitor
Also take note of prices on the JR lines:
http://www.japanrail.com/JR_japanrailpass.html
If you will primarily be in the Tokyo area then you are may want to visit the Tokyo Metro webpage for information on how to use that system including using the new PASMO electronic card system:
Tokyo Metro Home
Important Numbers -
Carry a list of important service phone numbers just in case you need help or run into trouble while in Japan. There are English speaking services available:
Important | Useful Telephone Numbers :: Japan Visitor
Cell Phones -
You will not be able to make it in Japan without a cell phone (keitai).
The "big three" cellular carriers in Japan are Au KDDI, NTT Docomo and Softbank. NTT Docomo is the largest of the three but Softbank boosts the most subscribers:
au KDDI -
au by KDDI
NTT Docomo -
NTT DOCOMO Global HOME
SoftBank -
SoftBank