U.S. Naval Base Guantanamo Bay - Crystal Cove State Park, 8471 N. Coast Highway, Laguna Beach, California.
Judge Advocate General's Corps – St. Elizabeth's Hospital's western campus, Redwood Street SE, Washington, DC. It was a federally run psychiatric hospital which later fell into disrepair although the east campus is still operational. The western campus now houses the headquarters of the Department of Homeland Security.
Lieutenant Junior Grade Danny Kaffee (Tom Cruise) plays baseball – 17th St SW and Independence Ave SW, Washington, DC. The ball field is no longer there. Many thanks to Tahoekid for the correction.
Danny and Sam Weinberg (Kevin Pollak) go to see Lieutenant Commander JoAnne Galloway (Demi Moore) – U.S. Department of Commerce (west side), 1401 Constitution Avenue NW, Washington, DC
U.S. naval base barracks Windward – Fort McArthur, Meyler Road, San Pedro, California
The Marine Corps War Memorial aka the Iwo Jima Memorial, Arlington, Virginia
Danny buys magazines and chats with the seller – Idle Time Books, 2410 18th Street NW, Washington, DC. The store has since then moved to 2467 18th Street NW but the alley where the newsstand was located in the film is still recognizable.
Sam's apartment building - 2415 20th Street NW, Washington, DC
U.S. Naval Base airfield - Naval Air Station Point Mugu, Oxnard, California
Colonel Jessep's (Jack Nicholson) house – Still searching for that location. Some sources claim it's Reservation Point in San Pedro but I can't confirm.
Danny's apartment – 3017 Dent Place NW, Washington, DC
Tidal Basin path and the Jefferson Memorial, Washington, DC
Danny pondering his moral dilemma – the Watergate Steps and the Arlington Memorial Bridge, Washington, DC
Lieutenant Colonel Markinson’s (J.T. Walsh)'s hideout – Downtown Motel (now Motel 6), 1345 4th Street NE, Washington, DC
The American President