alt.assassination.jfk - The most well-known discussion forum on the JFK assassination, although perhaps also the least polite.
The Education Forum -> Controversial Issues in History -> JFK Assassination Debate - Linked to from Spartacus Educational, which also has information and comments on the JFK assassination
History Matters - Pioneered online access to scanned government files, and linking detailed essays to the record. History Matters also sells document collections on CD-ROM. Site creator Rex Bradford is the MFF's senior analyst and archivist.
JFK Lancer Productions and Publications - Host to the annual November in Dallas conference, the Lancer website is chock full of essays, photographs, audio clips, and other information.
Assassination Archives and Research Center - The AARC has long been involved in the struggle to release government files on the case, and houses the largest private archives of JFK assassination records. Many of the MFF's records come from the AARC.
CTKA - Citizens for Truth about the Kennedy Assassination - CTKA published Probe magazine and has many of its articles available online, and is a good source for new developments in the 1960s assassination cases.
Harold Weisberg Archive Digital Collection - Harold Weisberg's documents and materials put online through the tireless efforts of Clay Ogilvie.
Baylor University Poage Legislative Library JFK Materials - The library holds donated collections from many prominent researches, with indexes and some scans online.
The Cold War Museum - Contains numerous resources on the Cold War, including the U-2 incident, the fall of the Berlin Wall, and the collapse of the Soviet Union.
Kennedy Assassination Home Page - The website notes that it is "dedicated to debunking the mass of misinformation and disinformation surrounding the murder of JFK."
National Archives - JFK Assassination Records - This portion of the National Archives website has finding aids and other information about JFK records, a search system, and online access to some documents.