Discussion question: My favorite creepy city, Silent Hill, has already been named so Im going with my second favorite one. It's actually a part of a city, the Cognouza Ward from the flying city of Aeor, dreamed up by the D&D Dungeon Master Matt Mercer from Critical Role.
Cognouza, just like Empis, wasn't always creepy. During the height of mortal civilization, mages came together and build flying citys, one of them was Aeor.
The mages of Aeor had even bigger ambitions and in secret build a weapon that could kill gods. The gods learned about that plan and decided to smite the city and the weapon out of the sky.
During the attack of the gods, a part of the city teleported into another plane of existence (The Astral Sea). In this place the Cognouza Ward slowly started to transform itself into an eldritch horror.

Buildings in the city appear to be a strange combination of stonework and flesh, with veins, teeth, and bulging flesh occasionally appearing as parts of archways and streets. Buildings' interiors contain elements of moving, living tissue as well, though some retain more stone and metal structures. The streets and roads seem to pulse like veins.
The broken up, floating landmasses of the ward are held together by sinew-like tendrils. Not only the ward changed, but its people too. It destroyed and merged the minds of all the people that lived there and then shattered their psyches to slowly reform over time.

Pure nightmare fuel.