Encyclopedia Smithsonian: American Indian History and Culture
http://www.si.edu/Encyclopedia_SI/History_and_Culture/AmericanIndian_History.htm
An information source for Art, Design, Museum Exhibitions, and more, as well as a comprehensive 'suggested reading' list.

First Nations Seeker: Directory of North American Indian Portal Websites
http://www.firstnationsseeker.ca
Visit First Nation and Native American Communities! Nations grouped linguistically.

Information on Individual Native Nations
http://www.nativeculturelinks.com/nations.html

Native Americans.com: Code Talkers
http://www.nativeamericans.com/CodeTalkers.htm
A brief background of the Navajo Code Talkers of World War II. See the left-side menu for more interesting topics from NativeAmericans.com.

Native Culture Links
http://www.nativeculturelinks.com/indians.html
A website dedicated to providing links to Native American Nations and organizations.

The Avolon Project: Treaties Between the United States and Native Americans
http://www.yale.edu/lawweb/avalon/ntreaty/ntreaty.htm
A website created by Yale University, providing primary documents--the texts of US/Native American Treaties--1778-1868.

University of Washington Libraries: Native American History
http://www.lib.washington.edu/subject/History/tm/native.html
This is a fantastic source for general history, as well as information about specific Tribes, broken down according to region. Also a good source of original documents and images.