The Thomas Jefferson Papers held by the Library of Congress are available online. Transcripts of the documents are not provided, only digital images, but the site also provides a small collection of scholarly articles, and a very thorough biographical timeline of Jefferson.
The University of Virginia library has created a "Thomas Jefferson Digital Archive" of more than 1700 documents, including a searchable collection of his writings and correspondence. The site also includes a virtual tour of the University of Virginia, as well as documents related to Jefferson's planning for the university. These materials can also be accessed through the Jeffersonian Cycolpedia—a searchable collection of Jefferson quotes and philosophical and political observations.
Jefferson's public papers and addresses are available through the Avalon Project at Yale Law School. His messages to Congress, inaugural addresses, and Notes on the State of Virginia are included in this collection. A small sampling of his private correspondence is also made available here.