(Part 4)
25. Shiga Prefecture

Love, Chunibyo & Other Delusions: Ootsu City

Donten ni Warau (Laughing Under the Clouds): Ootsu City

26. Kyoto-fu

K-ON!: Kyoto City

Tamako Market: Kyoto City

Inari, konkon, koi iroha: Kyoto City

Uchouten Kazoku: Kyoto City

Deaimon: Kyoto City

The Night Is Short, Walk on Girl: Kyoto City

Kyousougiga: Kyoto City

Hibike! Euphonium: Uji City

Kyoto Teramachi-sanjo no Holmes: Kyoto City

27. Osaka-fu

Ryuuou no oshigoto(The Ryuo's Work Is Never Done!): Osaka City

Hand Shakers: Osaka City

Magical Shopping Arcade Abenobashi: Osaka City

28. Hyogo Prefecture

This Art Club Has a Problem! : Himeji City

Wakaokami wa shougakusei (Okko's Inn): Kobe City

Fate/Stay Night: Kobe City

Sakamoto desu ga? : Nishinomiya City

Ghost in the Shell: Stand Alone Complex: Kobe City

Keijo: Awaji Island

Suzumiya Haruhi: Nishinomiya City

Grave of the fireflies: Nishinomiya City

29. Nara prefecture

Beyond the Boundary: Kashihara City

Red Data Girl: Totsukawa Village

Penguin Highway: Ikoma City

30. Wakayama City

AIR: Mihama Town

Binchoutan: Minabe Town

Binbougami ga!: Wakayama City

Lamune: Shirahama Town

31. Tottori Prefecture

Free!: Iwami Town

32. Shimane Prefecture

Blue Seed: Izumo City

Sguy & The Family Stone: Izumo City

33. Okayama Prefecture

Tenchi Muyo!: Okayama Prefecture

Hirune Hime (Napping Princess): Kurashiki City

34. Hiroshima Prefecture

Kamichu!: Onomichi City

Sora to umi no aida(Between the Sky and Sea): Onomichi City

Kimi no iru machi (A town where you live): Shobara City

Tamayura: Takehara City

Tanaka-kun wa itsumo kedaruge(Tanaka-kun Is Always Listless): Hiroshima City

Kono sekai no katasumi ni (In This Corner of the World): Kure City

Ponyo: Fukuyama City

35. Yamaguchi Prefecture

He Is My Master: Ube City

Mai Mai Miracle: Hofu City

Oku-sama wa Mahō Shōjo: Bewitched Agnes: Hagi City

The Wings of Rean: Iwakuni City

36. Tokushima Prefecture

Minori Scramble: Tokushima prefecture

37. Kagawa Prefecture

Karakai jouzu no Takagi-san (Teasing Master Takagi-san): Shoudo Island

Seto no Hanayome: Mitoyo City

Poco's Udon World: Takamatsu City

38. Ehime Prefecture

Mai:HIME: Matsuyama City

39. Kochi Prefecture

Poppin'Q: Nakatosa Town

Ocean Waves: Kochi City

40. Fukuoka Prefecture

Yuyushiki: Fukuoka City

Sketch Book Full Color's: Fukuoka City

Sono Toki, Kanojo wa: Fukuoka City

Sora no otoshimono (Heaven's Lost Property): Asakura City

Cooking Papa: Fukuoka Cuity

Kakuriyo: Bed and Breakfast for Spirits: Kitakyuushuu City

Hakata Tonkotsu Ramens: Fukuoka City

41. Saga Prefecture

Zombieland Saga: All across Saga Prefecture

Yuri!!! no Ice: Karatsu City

42. Nagasaki Prefecture

Barakamon: Goto City

Sakamichi no Apollon: Sasebo City

sola: Nagasaki City

Ao no kanata no four rhythm (Aokana - Four Rhythms Across the Blue): Goto City

Iroduku: The World in Colors: Nagasaki City

43. Kumamoto Prefecture

Natsume Yuujinchou: Hitoyoshi City

Aki no Kanade: Kumamoto Citu

44. Oita Prefecture

ReLIFE: Oita City

Prefectural Earth Defense Force: Oita City

45. Miyazaki Prefecture

Hyakko: All Across Miyazaki Prefecture

46. Kagoshima Prefecture

Robotics;Notes: Tanegashima Island

5 centimeters per second: Tanegashima Island

Princess Mononoke: Okushima Island

Umi monogatari: Amami

47. Okinawa Prefecture

Harukana Receive: Uruma City

BLOOD+: Uruma City

Haitai Nanafa: Naha City

Eureka Seven AO: Ishigaki Island

Asobi ni iku yo: Naha City

...Wait. It's almost 4 AM and I have work in a few hours. What am I doing? Sorry for the long comments.