Monticello, Jefferson's famous Virginia home, can be explored at this nicely constructed website. It includes an extensive collection of images—furniture, instruments, art, and architectural drawings—as well as narrated tours that explore the house, gardens, and "domestic life." There is also a gallery of Jefferson's inventions. Hosted by the Thomas Jefferson Foundation, the site has a digital collection of family correspondence, and also offers links to the Foundation report on the Jefferson-Hemings relationship.
The Library of Congress has constructed a website which explores the "extraordinary legacy" of Thomas Jefferson. It provides a useful introduction to the range of Jefferson's contributions and is illustrated with digital images from the Library's vast Jefferson holdings. The site also offers a detailed biographical timeline and provides a link to Jefferson Papers held by the Library of Congress which are accessible electronically to the public.
The Miller Center of Public Affairs at the University of Virginia maintains an "American President Online Reference Resource." The Jefferson site offers a series of short essays on Jefferson's life and career, as well as short biographical sketches of his vice-presidents and cabinet.
The companion site for Ken Burns' film on Thomas Jefferson is not particularly good, but it does include the complete transcripts of the interviews used in making the film.
Archiving Early America includes a "Jefferson Primer," a useful collection of short essays exploring his views on topics such as Native Americans, education, health, women, and the west.
For a look at how the presidential campaign of 1800 might have looked if twenty-first century technology had been available, check out this site.