"Quirky" has always been one of my favorite genres of TV series and movies, and such things often tend to be set in quirky towns. Mostly the quirkiness of the towns has to do with the quirkiness of the characters who live there, but the towns themselves can sometimes have some inherent quirkiness. So, here is a list of some of the quirky towns with which I'm familiar (mostly in TV series), and maybe a few quirky locations besides towns. (No doubt there are places I'm forgetting that I'd include here if I remembered them, as well as some places I'm not entirely sure qualify as "quirky" or not.)
Films
Beaverfield, (unknown state); from Werewolves Within
Mumford, Oregon; from Mumford
Spectre, (Alabama, maybe?); from Big Fish
(unknown town, unknown state); from Edward Scissorhands
Radio
Lake Wobegon, Minnesota; from A Prairie Home Companion
Television
30 Rockefeller Plaza, New York City, New York; from 30 Rock (Just one TV studio where everyone is kinda quirky.)
99th Precinct, Brooklyn, New York; from Brooklyn Nine-Nine (Just one floor of one police precinct, but I do consider it quirky.)
Chatswin, New York (presumably); from Suburgatory
Cicely, Alaska; from Northern Exposure (One of my all-time favorite quirky towns.)
Coeur d'Coeurs, (unknown state); from Pushing Daisies
Deepwater, Florida; from Maximum Bob
East Peck, South Carolina; from Trial & Error
Eureka, (unknown state); from Eureka
Evening Shade, Arkansas; from Evening Shade
Greendale Community College; from Community (Not a town, but the college definitely fits the trope.)
Hidden Hills, (unknown town, New Jersey); from The Neighbors (Just one gated community, where most of the residents are quirky for a very specific reason: they're aliens.)
LazyTown, (Iceland, maybe?); from LazyTown (this one I'm a bit iffy on)
Milford, Vermont; from Three Moons Over Milford
The Pit, Toronto, Ontario; from Liberty Street (Just one apartment building, actually called the Epitome.)
Ponyville, Equestria; from My Little Pony: Friendship Is Magic
Rome, Wisconsin; from Picket Fences
South Park, Colorado; from South Park
Springfield, (unknown state); from The Simpsons
Stars Hollow, Connecticut; from Gilmore Girls (One of my all-time favorite quirky towns.)
Twin Peaks, Washington; from "Twin Peaks" (I've never seen this show, but always wanted to)
(unknown town), Vermont; from Newhart
WNYX, New York City, New York; from NewsRadio (Just one radio station, but I consider its employees kinda quirky.)