Futari wa Pretty Cure is set in Wakabadai, an amalgam of various suburbs surrounding Tokyo on different sides. There is a real town by that name, but it's not anywhere particularly near Tokyo.
Yes! Pretty Cure 5 is set in a city that is supposedly somewhere in Japan. But it’s full of French signs, and some fans have noted that it looks like The Theme Park Version of London.
Dragon Ball is heavy on World Building, but it’s still not clear where on Earth much of the action is taking place. None of the nations are named or specified, and cities have names like “East City” and “Ginger Town”.
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Ojamajo Doremi has Misora Town (or “Misora City”), which is claimed to be in the Kanto region of Japan (i.e. near Tokyo). There is a real Misora Town, but that’s in Otsu, in the Kansai region.
Princess Tutu is set in the town of Kinkan, which is translated to "Gold Crown" in the English dub. But nearly all the text in the series is in German. Only in the last episode did we see a clue as to its location, where a town map named the town "Goldkrone" — German for "Gold Crown". This implies that it's either in Germany or a fantastic equivalent. It appears to be based on the real-life German town of Nördlingen.
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The town that D.N.Angel is set in is a strange case. All the characters have Japanese names and they seem to follow Japanese customs, but the town's architecture makes it look like a seaside European village. The anime added a character who claimed to be an exchange student from America, but otherwise countries aren't really mentioned. The audio commentary for the English dub has two of its voice actors asking, "Where is this set, anyway? France?"
It's never revealed what country the jungle in Haré+Guu is in. It does have Indonesian flowers, bears, and orangutans, but the rest of the wildlife is totally bizarre.
Prétear is set in the fictional Awayuki Town, somewhere in Japan. We're shown that the town appears to be on a small island connected to the main part of Japan by a bridge, but it's hard to tell much else.
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Mahou Sensei Negima! features Mahora Academy. All that can be determined of its location is that it's likely somewhere in the Kanto region of Japan (so somewhere near Tokyo).
Panty & Stocking with Garterbelt: Daten City and neighboring Oten City are equally vague. The setting itself is an Americasia, so while we see several Eagleland references, Daten City also has parts that look just like a Tokyo suburb.
Yu-Gi-Oh! is mostly set in Domino City, which is almost definitely somewhere in Japan. Some speculate that it’s a fictitious Tokyo. Yu Gi Oh Zexal takes place in Heartland City, and all we know about it is that it’s somewhere else in Japan.
Most of the race locations in Initial D are actual mountains, but Akina is a notable exception. It’s somewhere in Gunma and looks kinda-sorta like the real-life Haruna; beyond that, details are sketchy at best. The closest settlement is “S City”, which doesn’t help. The course in the manga also doesn’t match the Haruna course in the video games.
Umi no Misaki is set on what is for all intents and purposes a fictional small island in the vicinity of Okinawa.
Mitakihara, in Puella Magi Madoka Magica, is one of the stranger examples of this trope: there's a lot of very recognizable architecture, but it puts the series setting in thirteen different cities on four different continents. note Dubai, New York City, Taipei, Shanghai, Tokyo, Frankfurt, Singapore, Curitiba, Shinzuku, Milan, Cologne, Moscow, and Yokohama.
Is the Order a Rabbit? is supposedly set in Japan; everyone follows Japanese customs, eats Japanese food, and uses Japanese currency. But the town is modeled after Colmar, a town in Alsace – a region of France with a strong German influence, so there are both French and German influences in the show as well (like the German-style Christmas market). And the military rations shown in Episode 3 include things like raisin walnut, marshmallow fudge, and panna cotta, which the Real LifeKaiju Defense Force is unlikely to provide.
Much of the Nasuverse media is set in or around three fictional Japanese cities: Misaki, Fuyuki, and Mifune. Fuyuki is a coastal city modeled after Kobe, while Misaki lies further inland, near Tokyo. Beyond that, we know nothing about where they might be.
Most of Kiki's Delivery Service takes place in a city that explicitly borrows architectural elements from such locations as Stockholm, Visby, Lisboa, Naples, and Paris. It is implied to be located in Northern Europe, and the inhabitants seem to be a mix of European and East Asian phenotypes with no hint of racial segregation or discrimination. Word of God holds that Kiriko is basicaly a "Stockholm-in-a-world-without-WWII" with some other influences thrown in. Miya-sensei says that most of it is based on his notes and sketches from the time he visited Astrid Lindgren to discuss possible adaptation of Pippi Longstocking. The talks fell through,note The first Lindgren work to be adapted by Studio Ghibli is the Ronja the Robber's Daughter filmed by his son Goro Miyazaki some thirty years later. but the materials he obtained on the trip went into the movie.
Part of Your Name is set in Itomori, a fictional town in Gifu Prefecture, Japan that is based on the real-world Hida City, but is also next to a lake based on Lake Suwa in not that near Nagano Prefecture. Given Shinkai's pendant for Real Place Background, fans have tried to determine its location, but in Real Life there is only a swamp where it should be.
, but in Real Life there is only a swamp where it should be.
