Many thanks goes to everyone that have helped so far.

Many of the dramas are filmed at the same location.
Aoi Tori: Hokkaido, Kagoshima.
Ashita no Kita Yoshio: Kappa Tengoku in Yumoto-Hakone, Kanagawa Pref, Honshu In some of the scenes from ep. 5; When Heita-san goes to the "changing room" around 3:15 and also later when the assassin is talking to Heita-san's girlfriend, and when the investigator and his assistant are sitting the lobby hiding from the bypassing Heita-san. (posted by KuroRyu)
Hanazakari no Kimitachi e: Mizuki's house is in Ibaraki and not in California.
Hana Yori Dango 1 & 2: Makino's apartment is the same location setting for the dormitory scenes for the movie Honey & Clover (ハチミツとクローバー), which starred Sakurai Sho.
Ebisu Garden Square, Shibuya, Tokyo.
Eitoku Gakuen is actually Seikei University in Tokyo.
Domyoji's mansion is known as the British Hills in Fukushima Prefecture. (http://www.british-hills.co.jp/)
Hiroshima Showa 20 nen 8 Gatsu Muika: Hiroshima Peace Memorial Park.
Kurosagi: Kita Ward in Akabane Iwabuchi. (pictures, map)
Nobuta wo Produce: JAL Training Centre in Tokyo (pic 1, pic 2), Tokyo Marine University (pic 1, pic 2)
Papa to Musume no Nanokakan: Yokohama (pic 1, pic 2, pic 3)
Sexy Voice and Robo: JAL Training Centre in Tokyo (pic 1, pic 2)
Shikaotoko Aoniyoshi: Arashiyama, Kyoto, Bamboo Forest, Fushimi Inar Fushimi Castle, Nara Kouen
Tatta Hitotsu no Koi: Yokohama (pic 1, pic 2, pic 3)
Yukan Club: Yokohama (pic 1, pic 2, pic 3)
Credit: DramaWiki, IMDb, Erin Asakawa's Doramaworld including all others that have provied information/pictures.
List of filming locations (page in Japanese): http://loca.ash.jp/