The church where Admiral Fitzwallace (John Amos)'s funeral is held is St. Anne's Episcopal Church in Annapolis, MD - appropriate considering Annapolis is also the home of the United States Naval Academy.
The title is derived from Naval Support Facility Thurmont. Popularly known as Camp David, this is the president's mountain retreat where peace talks between the Israelis and Palestinians took place.
As President Bartlet is about to greet the Israeli Prime Minister, Abby Bartlet quietly says "Go get 'em, Cassius." Gaius Cassius Longinus was a Roman general best remembered as one of the plotters in the assassination of Julius Caesar. But Abby is almost certainly referring to the lesser known fact that before the assassination Cassius sought peace following the civil war between Caesar and Pompeius.
The name of the Israeli defense minister is Doron Mazar, there is a famous Israeli singer called Doron Mazar.
The American Flag on Marine One is upside down facing left, which is a sign of protest, in the shot with the Prime Minister.