Your first stop for any online Thomas Jefferson research. The Library of Congress (created when Thomas Jefferson sold Congress his own library) maintains this website for anyone interested in Thomas Jefferson. It includes timelines, online access to scans and transcripts of Thomas Jefferson's papers, supplementary essays, bibliographies, and a thorough (and trustworthy) list of links to other Jefferson sites and resources. Make sure to check out the Library of Congress's 2000 exhibition on Thomas Jefferson, under the "Related Online Resources" link.
A great resource for general Jefferson questions. Monticello.org runs this wiki for Jefferson scholars and specialists. All the information is vetted and reliable, and it covers all facets of Jefferson's life, from his family to his daily schedule. All cited information includes references. The parent site, Monticello.org, is run by the Thomas Jefferson Foundation, and includes a digital tour of Monticello, photos of Jefferson's houses, belongings, and grounds, various research reports, and a host of other Jeffersonian goodies.
The Jeffersonian motherlode. Maintained by the University of Virginia, the school he founded, the Thomas Jefferson Digital Archive includes access to the Jefferson Cyclopedia (a compilation of Jefferson's opinions, organized by theme, correspondent, and place), over 1700 documents produced by Jefferson, biographies, analytical essays, bibliographies, and too many other resources to list.
A wonderful little website which gives a snapshot of Jefferson and his presidential administrations through short biographies. Also includes links to some of Jefferson's works, a bibliography, and information on tracking down Jefferson's papers.
A companion site to Ken Burns' acclaimed documentary about Thomas Jefferson. It includes photographs, essays, which are not all that interested, and, transcripts of the interviews Burns conducted with the scholars for his documentary, which are very interesting. As a whole, the site isn't as thorough, or as useful as some of the other sites profiled, but it's not a bad resource.
From the time James Callender broke the story in 1802, until Nature published its groundbreaking paper on Jefferson's DNA in 1998, it was the raging controversy among Jefferson scholars. Did Jefferson engage in sexual relations with his slave, Sally Hemings? The debate can feel a little passé, but if you want to figure out what people were talking about, there really is no better place to start than here. Maintained by the Thomas Jefferson Foundation, this resource page has links to all the major documents in the "Hemings Controversy," including a wonderful "Brief Account" that offers a rich bibliography and a careful review of the evidence.