Neo-Tokyo in AKIRA is a classic and influential example in the genre. It is interesting the compare the colour pallet: Neo-Tokyo evokes the vibe while being much more colour-rich than the typical western example.
Silent Möbius is another series that inherits much of its city design from Blade Runner.
Zig-zagged by Tekkon Kinkreet's Treasure Town. It doesn't really look like a City Noir during the day — on account of all the sunshine and life. It is much less depressing than most examples, but it's definitely run-down, dangerous, and filled with people who can't stand living there. Ironically, the villain's plan is to turn the whole place into a family friendly amusement part by flat out murdering any hoodlums and street kids who don't follow the program.
Sin City: The venal Basin City (known as "Sin City" to the people who live there) and the seedy inhabitants who lurk in its alleys and doorway. It's almost exclusively set in and around Basin City's criminal underworld. Exaggeration unto high art.
Taxi Driver: It cannot be pressed enough how important this film was for this trope. An insomniac and depressed New York City cab driver becomes obsessed with cleansing the city of human "trash".
Coruscant, in Star Wars. Underneath (As in, literally, underneath; ground level up to around forty stories) the bright starships, the shiny skyscrapers, and the epic cityscape lies a planetwide hellhole of slums, filled with crime, despair, mutated monsters, as a result of widespread dumping of waste into the Underworld (as it is called) and general lack of maintenance by city authorities.
Another Fritz Lang film, M, also fits. It's a city where a paranoid citizenship have begun to attack anyone and everyone in search of a child killer, and the gangsters and police think dangerously alike.
Dark City is this setting taken to surreal heights through deliberate use of Diesel Punkby the city's alien overlords.
Every location in The Matrix trilogy, both in the real world and the simulated one, seems to be either one of these or a Wretched Hive.
New York in The Fifth Element uses the setting in an interesting juxtopostion with the rest of the movie which is generally light and playful.
Detroit/Delta City in RoboCop. Detroit is deemed as city "beyond saving", they want to tear it down and rebuild it as Delta City. Naturally, the place is a Crapsack World where the police force has been privatized and handed over to a Mega Corp..
Sweeney Todd: The Demon Barber of Fleet Street: Tim Burton's vision of Victorian London definitely fits the trope. Polluted streets and alleys, sewers with steam coming from them, dirty houses and dirtier rooms. The city is full of evil and corrupted people, including rapists, child abusers, serial killers turning people into cannibals, and so on and so forth. It's all visually very dark, as is usual in Tim Burton's works.
The unending, grim, grey town in C. S. Lewis' The Great Divorce. It's called "the grey town" and it's a dismal place where it is always twilight, the lights are on but are not welcoming, and it's always raining, even inside. The place seems empty and vast and there are too many houses. The place is crowd-less, and the only queue of people is at a bus station. Um... a very discomforting city.
Infamous' Empire City, a fictional stand-in for smaller New York. The city is quarantined due to an apparent plague, and there are three enigmatic gangs known as the Reapers, the Dust Men, and the First Sons who begin a turf war over the city. Empire City has areas in its sewer systems that can fit entire underground communities of homeless citizens.
The first level from The Punisher game from 2005 begins with a monologue about how even though the politicians have tried to clean up the city, all they succeeded in doing was pushing crime to other neighborhoods.
City 17 in Half-Life 2 was this on concept art in early stage of development, and it picked up a strong Eastern European inflection in the final work.
The urban locations in Kingpin: Life of Crime. Features everything between desolate ghettos and classy, but equally vile Radio City with it's Art Nouveau architecture (bearing a suspicious resemblance to some places in Payback). Also noteable for a weird mix of modern as well as 20's, 30's and steampunk-scifi styles (Cypress Hill music, Tommyguns, and thugs with cybernetic facial modifications all in the same setting!)
New Mombasa evokes one of these, though it was brighter and more welcoming before the Covenant invaded.
The City of Steelport in Saints Row The Third has art deco and industry seemingly running everywhere, and half of the time the game spawns you at night. Or in the rain.
Bezoar City of the obscure Cyber Punk shooter Hard Reset is perhaps the vastest, most towering example to be found on this page. When we say towering, we damn well mean it too; at certain points the wind whistles by fast enough to suggest you are a very... appreciable distance from the ground that you most definitely can't see. Yet, when you look up? There's still a lot more city to go. At least once you will go down the street through an industrial complex, only to find yourself on the ledge of a skyscraper.
Los Angleles in the Blade Runner video game. It's dark, rainy, and dirty.
The four nightmarish, Cog-swarming, gigantic Cog Headquarters in Toontown Online are very good examples, especially the Lawbot HQ, which appears to have an entire, New York-esque, city in the background.
The Jak and Daxter series has Haven City, a sprawling metropolis believed to be the last surviving city on the planet. It's heavily polluted, in a severe state of disrepair, and has a mafia that actively works with the city's evil government. By the time of Jak II, it's been under siege for hundreds of years, and the citizenry is impoverished and downtrodden due to the war and the Baron's tyrannical rule. On top of that, the government has secretly worked out a deal with their supposed enemy, the Metal Heads, to supply them with eco in exchange for attacking the city just enough to justify its continued rule. Did we mention that the Baron has a plan to destroy the Metal Heads that would also destroy the entire universe?
Batman: The Animated Series relies heavily on this trope for the stylistic views of Gotham City. And yes, it is often night, but that's when the bats take wing...
While the daytime shots of Republic City in The Legend of Korra are very beautiful, it turns out that the city hides a dark underbelly of crime and poverty. In particular, the night fight scenes in the streets take queues from this trope.
The same can be said to apply to Ba Sing Se of the original series, with secret agents of the government conspiring to keep the perfect balance they have created in the city, which also means keeping the hundred year world war secret to the public, and brainwashing anyone who dared to disrupt order.
Last Res0rt's City of Wonder. (although at least in terms of being a darkly colored city, they have the excuse of it being located inside a freakin' space station, so any sunlight or other weather that exists there is manufactured anyway...)
Moscow fits the trope perfectly, both in works like S. Lukyanenko's Watch tetralogy and in Real Life. The climate is dark and cold for nine months and blisteringly hot for the remaining three, the architecture consists mostly of drab Commie-era concrete towers with some neo-gothic Stalinist skyscrappers added downtown and a lot of squalid 'khrushevka' apartment houses in the outskirts, the citizens are apathetic, the Corrupt Corporate Executives are flamboyant jerks and the psychological athmosphere of the place was nasty enough even before the global financial crisis, and now it's downright unbearable.
St. Petersburg is similar to Moscow, but with extra gloomy clouds and extra gothic.
Other Russian major cities are Cities Noir, but with less decadence and more, often much more, of the city on the Wrong Side of the Tracks.
Glasgow, Scotland is the rainiest city in the UK. Similarly, it is full of drab, square council houses, with tower blocks puncturing the earth every now and then, derelict industrial works, some truly squalid City Narrows, with an old centre filled with neo-Gothic remnants of Empire. Dark as hell in the winter too. Subverting this trope, however, is the fact that the inhabitants are A: some of the cheeriest people in the UK and B: fiercely proud of their city, often getting angry and sometimes violent towards people who make it look - AAK!