These are collections of documents and images that are available solely online; there's no physical archive to visit. Not included here are more focused online collections, which explore a particular historical topic or theme. These are included in Readings - Online Exhibits.
Archives—digital and physical—have become an object of historical inquiry themselves. For an introduction, see Mike Featherstone, "Archive," Theory, Culture and Society 23 (May 2006) 591-596.
The Avalon Project, Documents in Law, History and Diplomacy (4000bce-2000+), Yale Law School
Europeana, showcasing cultural heritage from European museums, galleries, libraries, and archives; includes a collection on "Industrial Heritage"
Gallica, Digital Library of the Bibliothèque nationale de France
Digitale Texte im Seminar für Wirtschafts- und Unternehmensgeschichte, Universität Köln
Founders Online, papers of six Founding Fathers in the U.S. National Archives
Virginia Tech Libraries ImageBase—includes 12,000+ railroad photos
McGill University's In Pursuit of Adventure: The Fur Trade in Canada and the North West Company—offering a full-text searchable database of the Masson Papers