The Jefferson Digital Archive (UVa: a very comprehensive archive of Jefferson's letters, major works, and some digital images of the original documents. A great source for documents to search)
The Thomas Jefferson Papers (Library of Congress: see digital images of handwritten documents. Limited offerings but provides access to his personal documents in a way that used to require physical travel and special permission).
The Thomas Jefferson Papers: An Electronic Archive (The Massachusetts Historical Society: offers digital images of handwritten catalogue of books owned by Jefferson, hundreds of architectural drawings, and his original draft of the Declaration of Independence)