1. Name of Country
2. History
3. Geography
4. Culture
5. Travel

1. Name of Country

にほん・にっぽん・にほんこく
nihon / nippon / nihon-koku
日本・日本国
Japan
The Chinese characters (kanji) 日 means "the Sun"; 本, "origin"; and 国, "nation / country"

2. History

History by Periods / Themes

Portraits / Images of Japanese History

An Annotated Directory of Internet Resources: History of Japan

3. Geography

Japan: Facts and Figures
About.com: Geography offers general information on Japan including geography, population, politics and economy.

Columbia University East Asian Curriculum Project: Japan's Geography
provides comprehensive descriptions of geography of the region with relevant maps.

UCLA Center for East Asian Studies: Japanese Geography

4. Culture

a. Festivals & Holidays

• Japan-Guide.com: Annual Events
• Japanese National Holidays, Festivals and Events

b. Cuisine

• About.com: Japanese Food
• Japan Reference: Japanese Food

c. Clothing

• JP NET Kimono Hypertext

d. Art, Customs & Etiquette 

• Planet Tokyo: Culture Notes
• Kwintessential: Japan - Language, Culture, Customs and Etiquette
• The Clark Center for Japanese Art & Culture

5. Travel

Japan National Tourism Organization
Comprehensive site which introduces the country's history, culture, attractions and events, not only travel-related information

Japan-Guide.com: Japan Travel Guide
Thorough list of descriptions of regions, attractions, accommodation, transportation, food, and food etiquette
 
Lonely Planet: Japan Travel Information
The guide book website has beautiful photographs and videos of the country's sceneries along with the practical information on money & cost, weather and getting there & around.