https://www.youtube.com/watch?v=qlvPi09jVoA
I'll try listing them the ones below (brackets contain English names):
1. Hokkaido
Haiyore! Nyaruko-san: Sapporo City
Boku dake ga inai machi (Erased): Tomakomai City
Kanon: Sapporo City
Seitokai no ichizon: Sapporo City
Golden Kamui: All across Hokkaido
Servant x Service: Sapporo City
Sora no method: Toyako Town
Omoide no Marnie (When Marnie Was There): Kushiro City
Kimi ni todoke: Haboro Town
WORKING!!: Sapporo City
Saikano: The Last Love Song on This Little Planet : Otaru City
Sakurako-san no Ashimoto ni wa Shitai ga Umatteiru (Beautiful Bones -Sakurako's Investigation): Asahikawa City
2. Aomori Prefecture
Kumo no mukou, yakusoku no basho (The Place Promised in Our Early Days): Aomori Prefecture
Flying Witch: Hirosaki City
3. Iwate Prefecture
Inugami!: Morioka City
4. Miyagi Prefecture
Kannagi: Sendai City
Haikyuu: Sendai City
Wake Up, Girls: Sendai City
5. Akita Prefecture
Itoshi no Muco (Lovely Muco): Akita City
Kumamiko: Akita Prefecture
6. Yamagata Prefecture
Omoide Poroporo: Yamagata City
LEVEL E: Yamagata City
7. Fukushima Prefecture
Mikakunin de Shinkoukei (Engaged to the Unidentified): Kooriyama City
8. Ibaraki Prefecture
Girls und Panzer: Oorai Town
Momokuri: Mito City
Noucome (My Mental Choices are Completely Interfering with my School Romantic Comedy): Mito City
Sakura Trick: Inashiki City
9. Tochigi Prefecture
Yosuga no sora: Ashikaga City
Mokke: Tochigi Prefecture
Nasu: A Migratory Bird with Suitcase: Utsunomiya City
10. Gunma Prefecture
Nichijou: Isesaki City
Initial D: Mt. Akagi, Mt. Myogi
Sora yori mo tooi basho (A Place Further than the Universe): Tatebayashi City
Aku no Hana: Kiryu City
Houkago no Pleadas: Oota City