What I would really love to see is a comparative history online site that included Japan, China and Korea. Till then, here's what I found:
Ancient China: Through this site you can learn about ancient Chinese history, culture and philosophy.
East Asian History Sourcebook: From religious traditions to Imperial rulers, this site offers a great selection of links to help you learn about China, Japan and Korea.
Mysterious Mummies of China: This site is all about the Takla Makan mummies: where they came from, who they were, and the uses of mummification around the world.
Timeline of Chinese Dynasties: Chinese culture has existed for several millennia and is divided into numerous dynasties that you can find ordered and explained on this site.
Asian Studies Virtual Library: Learn more about the ancient and modern history of East and South Asian nations through the resources on this site.
Ancient Japan: Read through this site to get a great overview of Japanese history.