It's a city. Of spies.
These locations tend to occur in multi-polar 'verses (that is, with two or more power blocs) and are either neutral locations or the capital cities of the powers themselves.
If all the world's spies seem to work in the city a Spy Drama is set in, it's a City of Adventure. See also the Truce Zone, which is very often one of these.
Its vast number of spies might also be because a Deadly Decadent Court has set up shop here.
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Anime and Manga
Roanapur, in Black Lagoon, has a fair number of spies running around in addition to all the criminals.
Thanks to the mysterious Hell's Gate, Tokyo in Darker than Black is crawling with agents for every faction imaginable, from criminal cartels to national intelligence agencies.
One of the Marvelman/Miracleman comics ("Spy Story", #21 of the revived series, 1991, by Neil Gaiman) was about a woman living in a city of spies. Turns out all the members of the intelligence agencies of the world who couldn't adjust to the Utopia were put into one big city to intrigue their little hearts out.
Los Angeles serves as an interesting variation of this in Desolation Jones. It's a city full of spies who've all been forcibly retired and who are kept legally invisible by the government. They also can't leave.
Boktor (capital of Drasnia) and Mal Zeth (capital of the Mallorean Empire) in The Belgariad. Drasnia tops it all, being a country of spies. Spies are its chief export (that and reindeer).
King's Landing in A Song of Ice and Fire, though to a lesser extent than some of the other examples on this page, does have a large number of spies for different factions.
In Robert Sheckley's "Spy Story", there's an entire planet settled exclusively by the spies come to spy on the main protagonist.
Live Action TV
If you were to believe Burn Notice, Miami is full of spies and retired spies.
Then again, the city attracts a lot of retiring people and is pretty close to Cuba.
And it doesn't hurt that Florida doesn't have a state income tax, which makes it a popular place for mobile people to have as a residence.
Babylon 5: The station itself is a massive nest of intrigue, mostly because its the only neutral port around and between the major powers. Being the hub of diplomats means it attracts the dark side of diplomacy, spying.
Vancouver, of all places, on Intelligence (2006). This makes more sense than you might think. It's is a major world port right next to a major world power (the United States) and right across from two more (China and Russia) in Canada, which has traditionally served as a buffer between the three. Plus the fact that it's a very cosmopolitan city where any nationality blends right in, it could very well be a City of Spies for much the same reason Kathmandu has become so popular.
The Village in The Prisoner. All the inhabitants are forcibly retired spies.
Berlin in Pan Am. Of course as the series is set in the '60s, during the Cold War, as noted below this is Truth in Television.
Data East's Secret Service pinball suggests that everyone in Washington D.C. is either an undercover agent or a Soviet spy.
Top Secret, adventure "Operation: Sprechenhaltestelle''. The setting is a small neutral European town full of spies.
Al Amarja, the Mediterranean Banana RepublicOver the Edge is based in, is crammed to the rafters with weirdness of every description. The multiple espionage agencies fighting each other in the back alleys is one of the most mundane aspects of the setting.
Every player character in Paranoia is required to be a member of at least one secret society, and most NPCs are part of one as well. Given that the characters are supposed to be hunting down secret society members, this can get ugly.
Eberron goes a step further and has an entire country of spies - Zilargo, especially its capital of Trolanport. It's also the homeland of the gnomes. Adventurers in Zilargo are well advised to Beware the Nice Ones, as Zilargo boasts the most terrifyingly capable secret police force in the setting.
Planescape has Sigil, City of Doors, which is a city of spies because it contains portals to every plane in the multiverse and is therefore the most strategically important location imaginable. Legions of ideological/philosophical or political factions, religious groups, business empires, crime syndicates, and both sides in the Blood War have agents here.
In Knights of the Old Republic, Manaan in some ways has this role in its nature as an extremely valuable world that maintains neutrality. While both the Republic and Sith have embassies on the world, neither are allowed to carry weapons on the streets and are both extremely limited and forced to combat by proxy. In addition the trial of Sunry, where both he and his victim were being manipulated by the Republic and Sith, is an example of the types of manipulation that go on. The way in which the Republic builds a secret base with the approval of elements of the Selkath rulers also fits into this type of system.
Pottsylvania from Rocky and Bullwinkle is shown to be a whole country of spies in the few times it is shown.
Berlin (Cold War) because it was a city in the middle of communist territory where all four occupation powers were in close proximity (as was Vienna, see below).
Lampshaded in all conceivable versions of Casino Royale by Bond girl Vesper Lynd.
The opening video on the National Spy Museum tour estimates that DC has more spies per capita than any other city on the planet.
Which causes problems when selecting areas for dead drops or covert meetings between spies and their handlers. Because thousands of spies have been working in cities like Washington and Moscow for over half a century, there's very few 'ideal' locations that haven't been used before. In theory a security service could stake out these places permanently and have a good chance of catching a spy in the act.
Also during the The American Civil War, with DC set between Confederate Virginia and Confederate-friendly Maryland and a good number of residents sympathetic to the Southern Cause. DC's mirror opposite city, the Confederate capital of Richmond, Virginia, was riddled with Union spies and sympathizers,note Virginia was very reluctant to secede and one of the last to do so and join the Confederacy and perhaps more to the point, all of the slaves in Richmond—including those in Confederate President Jefferson Davis' own household—were natural Union sympathizers and therefore natural Union spies (Davis' housekeeper, for instance, was a Union agent).
Depicted as a nearly literal City of Spies in From Russia with Love.
Helsinki (Cold War): Because it was close to the Soviet Union, largely sympathetic to the West, but neutral. The Finns were quite aware of their situation, practicing a policy of "bowing to the East in such a way that it could not be seen as mooning the West."
Tallinn, Estonia (Today), because it was once part of the Soviet Union, but is now firmly in the Western camp (part of the EU and NATO). Since 2008 the city is home to the NATO Cyber Defense Center. This last is not particularly surprising: Internet penetration in Estonia is ridiculously high (the country was the first to hold official online elections), the country has a large number of internet-based companies, and Estonian systems are a common target for Russian hackers.
Kathmandu (For the last decade or so): With Nepal being sandwiched between the two next likely superpowers, and a strategic prize for either, the capital has become like this. Sympathetic towards India mostly, but makes sure to keep Beijing in the loop.
Vienna (Cold War). Most people don't realize this, but Austria, like Germany, was carved up into four occupation zones after the end of World War II, with Vienna also being divided. The terms under which the occupation of Austria ended mandated that Austria become a neutral state, which it did, so its situation ended up being rather like Finland's. Also, a large number of international institutions are based in or have major offices in Vienna; of these, the most important are the International Atomic Energy Agency (IAEA) and the Organization of Petroleum Exporting Countries (OPEC).
Iga, Japan (Feudal ages): It's where ninjas originated and where most of them lived during the feudal ages in Japan. It became so independent of the rest of Japan that it became a de-facto city state until 1581, when it was destroyed.
Prague seems to be the setting of many tales of espionage and intrigue across several genres.
London particularly during World War II when it was the main staging ground for the war efffort but other periods as well. During the Cold Warnaturally and the early days of the age of sail, both CivilWars and half a dozen other time periods, the place was swimming with people selling information to all sides of these conflicts. It probably has dozens of spies in residence to this day due to being one of the largest and most influential cites in the world.
Vientiane, Laos in the 1960's thanks to its unusual coalition government of neutralists, communists and right-wingers, formed because JFK's administration didn't want to risk a direct confrontation in the region. Instead all sides waged a proxy war through the various Laotian factions until the communist forces became powerful enough to take over by military force in 1975.