Landmarking the Hidden Base

A hidden base would probably be best hidden in some bland ubiquitous building or under some random field or street. After all, bases would be easier for the enemy to find if you give them easy points of reference.

However in fiction that simply isn't dramatic enough, not only does your Evil Tower of Ominousness gain Evil Brownie Points for being cool and domineering, it also gains them if it is actually a well known Real Life landmark you've taken over. An Elaborate Underground Base also gains kudos for being underneath, or very close to, somewhere with which viewers will be familiar. This actually goes both ways as heroes seem just as prone to settling in such a location as villains are.

Mount Rushmore is an oddly popular location; perhaps because it's easy to imagine those presidential heads not being made up of solid rock but instead holding masses of secret rooms inside. It must get awfully crowded in there.

Note this trope does not cover bases in or under fictitious landmarks like The Fantastic Four's Baxter Building or "almost" landmarks like "The Jeffersonian Institute" in Bones. It also does not cover a fictional agency openly using a landmark as their base, such as UNIT operating out of the UN building in Doctor Who.

Of course this makes a Monumental Battle all the more likely to happen if and when the series has the base attacked.

Also see Weaponized Landmark, where the landmark shoots back...

Anime

 * In X 1999, The Dragons of Heaven has their headquarters under the Diet Building, while the Dragons of Earth reside under the Tokyo Government offices.
 * Read or Die has its network of superspies based in a secret underground lair beneath the British Library. Justified in that they also work for the British Library.
 * Digimon Tamers used several floors of the Tokyo Metropolitan Government Building as HQ for HYPNOS.

Comic Books

 * In The DCU, the All-Purpose Emergency Squad (APES) had its headquarters inside Mount Rushmore.
 * In The League of Extraordinary Gentlemen, the League's headquarters is inside the British Museum.
 * The Runaways second "Hostel" is an Elaborate Underground Base underneath the La Brea Tar Pits; it used to belong to their evil parents.
 * Mr. Majestic, Wildstorm's Alternate Company Equivalent of Superman, has his headquarters inside (where else?) Mount Rushmore.
 * The Quorom, an all purpose evil organization from The DCU, had one of its main bases under the Reflecting Pool in Washington, D.C. (and a villain containment pod under the Washington Monument). Not quite a good idea when heroes smash in through the roof.
 * A Fantastic Four tie-in novel had a supervillain (The Mad Thinker) craft a base in Mount Rushmore. Cue Reed sliding out of a nose. In the regular Marvel Universe, Mount Rushmore just tends to get blown up. Yes, more then once.
 * The All-Star Squadron were based in the Trylon and Perisphere from the 1939 New York's World Fair. The Perisphere was their headquarters, and the Trylon was their Cool Garage.
 * In Peter David's Spy Boy, the "good" spy team (this troper can never remember if they were S.H.I.R.T.S or S.K.I.N.S) had their invisible headquarters suspended between the tops of the twin towers of the World Trade Center. (This got moved later, for obvious reasons.)
 * In Invincible spinoff Guarding the Globe, Cecil shows team leader Brit around a new Guardians of the Globe satellite base—inside Big Ben. Brit isn't sold on the idea, and Cecil suggests having the Sphinx hollowed out to make room for a base there, too, maybe with a jet hangar. Brit can't tell if he's joking or not. He wasn't; a couple of issues later it's revealed that this is exactly what he did

Film

 * Team America: World Police has the base in Mount Rushmore again.
 * The villains in North by Northwest have a house on Mount Rushmore's peak.
 * In the Austin Powers movie The Spy Who Shagged Me Dr. Evil has a base in the Space Needle.
 * And in Austin Powers in Goldmember, Dr. Evil's base is behind the Hollywood sign.
 * The first live-action Transformers movie had the FBI keeping Megatron and the All Spark inside Hoover Dam, which in the story was actually built to block out the Allspark's energy signature...or something.
 * In National Treasure: Book of Secrets the ancient mythical city of Cíbola was hidden behind Mount Rushmore. Or rather Mount Rushmore was created to hide Cíbola.
 * The huge movie studio in The Truman Show was behind the Hollywood Sign.
 * Of course, there's nothing hidden about it, given that it's a gigantic dome clearly visible from space.
 * Q the Winged Serpent nests in the top of the Chrysler Building in New York City.
 * CONTROL headquarters was under the Smithsonian Castle in Get Smart.
 * The Man with the Golden Gun: The wreck of RMS Queen Elizabeth is used as an MI6 base.
 * Captain Invincible had a hidden base in the head of the Statue of Liberty... when he wasn't drunk off his mind in the Australian outback
 * In the Judge Dredd film, Rico's secret cloning lab is located in the head of the Statue of Liberty.

Literature

 * In the Doc Savage novel World's Fair Goblin, the villain has his secret lab hidden inside the Trylon and Perisphere at the New York's World Fair.
 * Doc himself lived on the top floor of the Empire State Building.
 * Kim Newman's pulp homage/parody character Dr Shade apparently lives in a "secret" apartment in Big Ben. Since in Newman's world he's both a real adventurer and a magazine character (in a sort of takeoff of the Literary Agent Hypothesis), readers of the magazine wonder why it's described as secret.
 * Arsène Lupin's base in the Hollow Needle happens to be inside the Étretat Needle, a natural landmark of the Seine-Maritime.

Live Action TV

 * Stargate SG-1 had the Stargate under Cheyenne Mountain, which was the real-world home of NORAD. NORAD has since moved, but the Cheyenne complex is kept on warm standby.
 * Justified up the wazoo by the fact that this is an actual military base, so sticking a military base in it is hardly surprising.
 * There's supposedly a door in the actual base marked "Stargate Command", though noone seems to have a key for it...
 * There really was such a door and it was a broom closet.
 * Neil Gaiman's Neverwhere has an entire culture of "lost" people and things inhabiting the various stops of The London Underground.
 * Averted in Roswell. For some reason, the government keeps alien spaceships in secret basements under convenience stores, and in movie studios.
 * Buck Rogers in The 25th Century had a second season episode in which Buck was accused of having helped foment the big nuclear war in the late 20th century. A device to visualize Buck's memories seems to confirm his guilt, but he keeps flashing on Mount Rushmore. Buck manages to get to Mount Rushmore and finds that the President had a secret bunker inside.
 * The Canary Wharf Tower one was done by the 90s remake of The Tomorrow People. The reasoning was that the immortal Egyptian villain needed to hide a power-focusing pyramid in the middle of London, hence the pyramidal top of the tower.

Doctor Who
"Donna: What, there's like a secret base hidden under a major London landmark? The Doctor: I know, unheard of..."
 * The Torchwood Institute has had bases:
 * In One Canada Square (a.k.a "Canary Wharf Tower") in "Army of Ghosts"/"Doomsday".
 * Under the Thames Barrier in "The Runaway Bride", where it's Lampshaded:


 * Under Roald Dahl Plass, near the Millennium Centre in Cardiff, where The Hub is based in the Whoniverse spin-off Torchwood (and in "Utopia", "The Stolen Earth" and "Journey's End").
 * UNIT had one: Under the Tower of London in "The Christmas Invasion". It beat their early place that had a conspicuous "Keep Out" sign.
 * Various bad guys have based themselves in/under:
 * Gatwick Airport (The Chameleons in "The Faceless Ones")
 * The Post Office Tower (WOTAN in "The War Machines")
 * The London Eye (The Nestene Consciousness in "Rose")
 * The Empire State Building (The Cult of Skaro in "Daleks in Manhattan"/"Evolution of the Daleks")
 * They make an attempt to justify many of these, explaining there is something important about the location or nature of the structure that they need. For example, the Torchwood Tower (Canary Wharf) exists because there was a rift high in the air, so they had to build a giant tower to reach it, The Hub's location was chosen due to its proximity with yet another rift and the Nestene Consciousness was using the London Eye as a giant transmitter to broadcast the signal controlling the Autons. In "Daleks in Manhattan", the Daleks attached Dalekanium strips to the top of the Empire State Building (which at the time was the tallest building on Earth) to kick-start a new race of hybrids with a solar flare.
 * Canary Wharf is also the headquarters of the British time travelling military in an alternate 2006 visited by the First Doctor in the Past Doctor Adventures novel The Time Travellers. And the villain of the Sixth Doctor Missing Adventures novel Millennial Rites (for reasons broadly similar to the Tomorrow People villain).

Video Games

 * In Tom Clancy's Rainbow Six: Vegas, a top-secret Army Weapons Research Lab is located inside the lower levels of the Hoover Dam, which contains numerous highly dangerous weapons and vehicles. Why they just didn't do the research at nearby Area 51 isn't explained.
 * That's the first place everybody would look.
 * Similarly, in Tom Clancy's Ghost Recon: Advanced Warfighter 2 apparently a computer system linked to the United States anti-ballistic missile defense grid's mainframe is located under a dam in El Paso Texas.
 * Nearly everything in Fallout 3, since the game takes place in Washington, D.C. After the End. The most recognizable are probably the Washington Monument (Brotherhood of Steel and Three Dog's communications relay), the Pentagon (Brotherhood of Steel), the Mall and Museum of Science (Super Mutants), Museum of History (Ghouls), the Jefferson Memorial (Project Purity), the Lincoln Memorial (Slavers and eventually freed slaves), the ruined Capitol Building (in some ways the Bonus Dungeon), and the White House Crater.
 * Justified with the Pentagon and the Lincoln Memorial. The Brotherhood chose the Pentagon both because it was easily defensible and because it contained plenty of pre-War technology (including ). The slavers don't want slaves to be exposed to anything related to Abraham Lincoln.
 * In Deus Ex, UNATCO's HQ and therefore  are both built on Liberty Island.
 * This one is justified in game as a symbolic decision. UNATCO was founded in response to a terrorist attack that destroyed the Statue of Liberty.
 * STALKER is all about the terrible secret at the center of the Zone of Exclusion, buried deep within the Chernobyl Nuclear Power Plant.
 * Conspiracy Theorists might also get a shudder at the inclusion of the Duga-3 Over-The-Horizon-Radar array's inclusion, known in Number Station circles as the Russian Woodpecker, suspected by some as being a Mind Control Device or Weather Control Machine. In the series, it does both.
 * Not to be confused with the Brain Scorcher from the first game, which is merely based on the Duga-3.
 * In Evil Genius, a rival genius tried to build an underground lair inside the Great Wall of China, consisting of a single corridor.

Web Comics

 * Though they maintain more conventional safehouses, The Chain in Necessary Monsters maintains a base under the Statue of Liberty called Liberty's Price. It's a huge cavern with occult symbols, and an inverted, chained, tortured version of the Statue of Liberty as its centerpiece. However, Liberty's Price is implied to be older than the landmark built over it.

Western Animation

 * Ben 10 has The Plumbers base be inside the ever-popular Mount Rushmore.
 * In one episode of Phineas and Ferb Dr. Doofenschmirtz has a hidden base inside Lincoln's head at Mount Rushmore.
 * In Spider-Man: The Animated Series, the Kingpin's lair is in the Chrysler building. There's a secret underground entrance so people not in the know won't find out where his base is (even though the lair's high ceiling looks like the interior of the Chrysler Building's spire might be expected to look). Of course, by five seasons later, enough airborne bad guys have waltzed in and out that someone oughta suspect that something about that nice philanthropist Wilson Fisk isn't kosher.
 * Parodied on The Venture Brothers. The Monarch brags about how his base is in such a secret location that he flies by radar alone to get there, that it could be anywhere and nobody would find it...except that it's in the Grand Canyon and very visible.
 * Parodied on The Simpsons. In one Treehouse of Horror episode, a missile launch pad is under the Eiffel Tower.

Real Life

 * The White Cliffs of Dover hide a network of formerly secret underground tunnels.
 * Gustave Eiffel built a private apartment for his own use on top of the Eiffel Tower in Paris.