Theater in general in Japan offers an abundance of riches. An introduction to traditional forms of dramatic entertainment can be found at a site maintained by the city of Kanazawa; beyond the basic overview provided, the site also explores several theatrical forms in greater detail.  Angela Tse's essay on "Performing Arts of Japan" is another good place to start your exploration.
 
Japan's dramatic tradition extends back in time to the earliest forms of dance and worship performed at court or in the presence of local Shinto deities.  Gagaku, an aristocratic dance form originally imported from neighboring China, is still preserved in Japan today, its elaborate costumes, stately choreography and stylized gestures clear antecedents for many later theatrical forms.

Many sites specialize in one of the three most common forms of traditional theater -- Noh, Bunraku or Kabuki.  One extensive outline of all these as practiced in their earliest forms can be found in the extensive web pages devoted to the theater arts in Mediveal Japan, a course taught at Nebraska Wesleyan University in the Spring of 1998.

One site devoted to Noh, a traditional aristocratic form of drama, is maintained by a group of dedicated fans. Much of the information here is in Japanese; however, also included is a beautifully illustrated introduction to Noh and Kyogen (Kyogen is a comic play form often performed with Noh).  Don Herbison-Evans (from the University of Sidney) provides a detailed discussion of Noh dance in a nicely-done illustrated essay

Bunraku today is a term generally used to apply to many forms of traditional puppetry.  Tsang Shuk Wa (writing for the Japan National Tourist Organization) provides a good overview in his article "Actions Speak Louder Than Words in Japanese Puppetry" while Matthew Johnson provides an extended historical overview as part of his contribution to The Puppetry Home Page.  The Daily Yomiuri Newspaper site includes a detailed consideration of the many elements of Bunraku useful for those interested in further exploration.

Doi Junichi, a Professor of Classical Japanese Literature at Ryukoku University in Kyoto, maintains a site including a number of illustrated examples of puppets and a section outlining the construction of an "unmarried female puppet".

The island of Awaji has its own well-developed puppet tradition, and the students in the Performing Arts Club at Mihara Senior High School have been enlisted to carry on the tradition into the next millenium -- an inspiring story!  So, too, the Tonda Traditional Japanese Puppets have an interesting story behind their origins -- and their own attempts to maintain the tradition into the next generation.  Other independent traditions to examine include the Sarukura Puppet Show (with its wonderful collection of photos) and the Awa puppets from Tokushima on the island of Shikoku.

Many other forms of wooden dolls related to those associated with the puppet theater also exist in Japan.  The best place to find out more is at the Lotz Wood Dolls site maintained by Jean D. Lotz.

A good overview of kabuki theater is provided by the The International Society for Educational Information, Inc. in Tokyo, but the best place to begin your exploration of Japan's most famous form of traditional theater is really with a visit to Kabuki for Everyone, which introduces this popular drama exceptionally well.