The Library of Congress This site has many primary sources organized by collections.
The Gilder Lehrman Institute of American History. Great timelines by periods and documents by time period.
American Memory Timeline -- Further help from the Library of Congress. These documents are organized chronologically.
Information about the Nuclear Age and the Cold War at Atomic Archive.
Presidential Libraries are good sources for primary documents.
Smithsonian Source -- Resources for American History
Top Ten National Archives Websites This site has links that makes it easier to locate what you want in the National Archives' 10 billion information item. Educator resources from the National Archives.
NARA 100 Milestone Documents You may find something you need in this list of 100 important American primary source documents.
Calisphere This site is a good source of primary documents and images -- many of them relate to California and the Western part of the United States history.
http://www.consource.org/ Constitutional history
https://www.loc.gov/rr/mss/teachers.html Library of Congress Online Primary Sources from Manuscript Division Collections
https://www.documentcloud.org/home A catalog of primary source documents and a tool for annotating, organizing, and publishing them on the web.
https://history.house.virginia.gov/capitols Everything about the members of the Virginia House of Burgesses from the beginning
https://www.hathitrust.org/digital_library Lots of digital documents provided by various digitizers, including Google.
Cold War Primary Sources,
The Crusades Primary Sources,
Chronicle of the Russian Tsars.
Do NOT select primary documents from answers.com or other general information websites, but go back to a reliable primary source website.
http://www.bl.uk/manuscripts/Default.aspx Digitised copies of manuscripts and archives in the British Library’s collections, with descriptions of their contents. Continually updated.
http://www.fordham.edu/halsall/sbook.html Internet Medieval Sourcebook from University of North Florida and Fordham University
An Eyewitness to History This site has photos, video clips and other documents from people who lived through history. The historical documents cover both U.S. and world history through several centuries through World War II.
The World Digital Library offers access to primary materials from countries and cultures around the world. Primarily offers links to prints and photographs.
Euro Docs "...connect to European primary historical documents that are transcribed, reproduced in facsimile, or translated." (Documents are not always translated.)
Library of Congress exhibits Creating French Culture: treasures from Bibliothequè Nationale de France
http://history.hanover.edu/project.html Translations of scanned texts from ancient to modern times.
http://www.centropa.org/ History of European Jews
Eurodocs European History
http://www.luminarium.org/ Anthology of English literature
manuscrits-france-angleterre Explore 800 medieval manuscripts
of France and England
Specifically religious, although look above as well
http://anglicansonline.org/index.html Anglican literature and history