The Thomas Jefferson Papers held by the Library of Congress are available online. Transcripts of the digital documents aren't provided, but the site also provides a small collection of scholarly articles, and a very thorough biographical timeline of Jefferson.

The Jeffersonian Cycolpedia is 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.