Starfleet Headquarters was the administrative center of Starfleet Command located in California, on Earth. Sharing grounds with Starfleet Academy, it encompassed territory adjacent to the city of San Francisco, on either side of the Golden Gate passage into San Francisco Bay.
The sprawling complex was originally built as the headquarters of the Earth Starfleet in the early 22nd century, on what was previously a portion of Golden Gate National Recreation Area in Marin County, overlooking Horseshoe Bay. After the founding of the United Federation of Planets in 2161, it continued to serve as the command center of the Federation Starfleet. By the 2270s, the headquarters had expanded to the Presidio, an ancient military post on the southern side of the Golden Gate, where it included an air tram station. (Star Trek: The Motion Picture)
In 2293 the senior crew of the USS Enterprise-A attended a meeting in a briefing room at Starfleet Headquarters regarding the following peace talks with the Klingons. (Star Trek VI: The Undiscovered Country)
In 2369, Odo tried to contact Starfleet Headquarters to tell them about the situation on Deep Space 9. However, Major Kira Nerys had ordered all subspace communications to the Federation be blocked. (DS9: "Dramatis Personae")
In 2371, Benjamin Sisko was debriefed on the Dominion situation in Starfleet Headquarters for several weeks. Sisko also enjoyed visiting it, hoping to be an Admiral based there one day. (DS9: "The Search, Part I")
Rear Admiral Bennett, the Judge Advocate General, had an officer at Starfleet Headquarters. He told Richard Bashir to report there in later in 2373, when he arrived on Earth from Deep Space 9. (DS9: "Doctor Bashir, I Presume")
In 2374, the Emergency Medical Hologram known as The Doctor spoke directly to Starfleet Headquarters after securing the USS Prometheus from Romulan forces. Informing them that USS Voyager was stranded in the Delta Quadrant, Starfleet Headquarters returned The Doctor to Voyager with a message for its crew - "You are no longer alone". (VOY: "Message in a Bottle")
Logistical Support was an office at Starfleet Headquarters that specialized in technology support. The office was located in Headquarters' main complex, through the second door on the right. The office was a secure area, and devices such as holo-imagers were not allowed. (VOY: "In the Flesh")
In late 2375, during the Dominion War, Starfleet Headquarters was attacked by the Breen. Buildings were badly damaged, including the historic Golden Gate Bridge, and many people were killed. (DS9: "The Changing Face of Evil", "When It Rains...") By 2376, the city had been restored to its original appearance. (VOY: "Pathfinder")
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after the Breen attack of 2375
The Starfleet Headquarters grounds were filmed at the Tillman Water Reclamation Plant in Van Nuys, California, where the Starfleet Academy scenes were also filmed. Matte paintings were typically added to enlarge the overall scenes.
The Presidio Starfleet Headquarters Maquette
While the exterior footage of Presidio Starfleet Headquarters in DS9: "Homefront" could have been easily misconstrued as being largely a matte painting, that was in this case only true in a small part. Most of the view was in actuality a composite of life footage of the Tillman Water Reclamation Plant in Van Nuys, Ca., embellished with footage of maquettes, constructed for background-, as well as foreground elements, edited-in in post production into the final shots.
The design of the overall look was in the end a collaborative effort. Doug Drexler recalled in awe the General Motors Pavilion of the 1964/1965 World Fair, he had seen as a child, "The General Motor’s pavilion was one of the largest buildings at the fair. Approximately 4.000 tons of structural steel and 10,500 cubic yards of concrete went into it’s construction. The distinctive canopy that served as the pavilions entrance soared 10 stories over a reflecting pool, and was visible for miles. Housed within was the popular Futurama ride, which predicted moon bases and vacation hotels under the sea. It was a huge inspiration to thousands of kids who grew up to be scientists, engineers, and yours truly. Many years later in the DS9 episode Homefront, VFX supervisor Gary Hutzel called Mike looking for a model of starfleet command yesterday. The GM pavilion came instantly to mind. To me, the soaring canopy reminded me of the billowing sail of a ship of the line. I showed it to Mike, and he handed it over to Anthony Fredrickson. Anthony slammed it together using an old levelor blind and spare parts. The train was made out of bird feeders and cassette racks. Considering he had no time, he did a marvy job, but it was not as elegant as I would have liked. Still a kick." 
Fredrickson, upon who the actual construction work fell, recalled that they had "only a couple of days and a budget of zero". However as he continued,
"Doug Drexler instantly grabbed for some inspiration. Pinned to the wall by his desk he had a souvenir pamphlet from the 1965 World's Fair. It showed the General Motors pavilion, which is the architectural definition of 'Star Trek'. I had the construction guys cut and shape me an appropriate piece of "wiggle wood", a bendable kind of plywood. To me, the building's facade looked like a curving venetian blind. It was a simple matter to walk across the lot and liberate a dusty set of blinds from an empty office. The front of the model was lined with the thin metal slate, and the overall effect was like a tall, narrow, drive-in movie screen, hung with the Federation of Planets logo. At the front of the building we modeled a park crisscrossed with walkways, and used Micro Machine starships to represent sculptures, like the way a military base will mount an old jet outside the entrance.
Mike Okuda brought in two freestanding compact disk storage racks he figured would make excellent high-rise office buildings One of the racks looked to me like a tunnel for a high speed magnetic tram. We used it in the foreground horizontally along the ground. The perfect tram car was discovered in a plastic and aluminum hanging bird feeder. Its streamlined shape fit nicely in the tunnel, and after a little paint and pinstriping it provided the illusion of expansive windows and sliding doors.
The models were composited with life footage of the Tillman Water Reclamation Plant in Van Nuys, which had already stood in for Starfleet Academy in an episode of Star Trek: The Next Generation. I was told you can just see the Golden Gate Bridge in the distance, but I never saw the episode. Did they make the tram car zip through the tunnel like they promised? I sure hope so." (Star Trek: The Magazine Volume 1, Issue 13, p. 112)
Indeed, the tram Fredrickson referred to, was actually constructed, and it was intended by the Art Department as a subtle homage to Gene Roddenberry's aborted Earth II pilot. Confirming Fredrickson's remarks, Michael Okuda stated that the tram and tunnel assembly was based on, "a couple of CD holders and a hummingbird feeder bought at a gardening shop". Likewise Judy Elkins commented, "It was just a bunch of metal arches". The tunnel look was created in post-production by digitally painting in the reflections and highlights that made the spaces between the arches look like Plexiglas. This was done at Digital Magic by Computer Animator Adam Howard. "He even animated a blinking light to the "tube", to make it look as if a yellow light went on and off when the tram came through.", Elkins continued. The Golden Gate Bridge, visible in the background, was not a part of the background matte painting, but an actual photograph Effects Supervisor Dan Curry took of the bridge. Footage of the two maquette pieces were shot at Image G and all individual elements were composited in post-production at Digital Magic into the final shot, overseen by Visual Effects Supervisor Gary Hutzel. (Star Trek: Deep Space Nine Companion, p.302)
The maquette which constituted the sail backdrop of the main building of Starfleet Headquarters had in front of it mounted silver plated Micro Machines representing members of the Template:ShipClass, Template:ShipClass (original and refit) as well as the Template:ShipClass. The maquette itself, measuring 48x29x13in, was eventually offered up as Lot #481, part of the 40 Years of Star Trek: The Collection auction and estimated at US$1,000-$1,500, being eventually sold on 6 October 2006 with a winning bid of US$5,000 (US$6,000 including buyer's premium).