There are a huge number of locations, and as I have only 5 days I will not be able to visit them all (or let's face it, even a quarter of them), though I hope to visit as many of the Tokyo, Osaka and Kyoto locations when I am in those cities with my classmates.
Odani Castle ruins on Lake Biwa (where Gou was born)
Hikone Castle, Lake Biwa
Ohmi Mariner’s Lake Biwa Ferry from port Hikone. Lake Biwa Ferry from Port Nagahama or Port Imazu.
Isu Gifu of Mie Prefecture
Iga- Ueno Castle Mie Prefecture also the location of a Ninja Museum
Tsu Castle/Anotsu-Jo Castle Mie Prefecture
Temple of Ise
Tamaru Castle, Tamashiro town, Inabe County, Mie Prefecture.
Nagoya Castle, Aichi Prefecture, Chubu Region
Kiyosa City, Aichi Prefecture.
Fukui City, Fukui Prefecture
Eiheiji Temple, Fukui City
Maruoka Castle, Fukui City
Shibata Shinto Shrine, Fukui City
Mt Asuwa Fukui City
Shizugatake, Ōmi Province, near Lake Biwa
Genbao Castle玄蕃尾城, on the ridge of Yanagaseyama mountain, one of 450 meter height above sea level located at the border of Omi province (Shiga prefecture) and Echizen province (Fukui prefecture).
Lake Yogo, Ika district, Shiga Prefecture
Ōtsu castle (60,000 koku) in Ōmi province, Shiga Prefecture
Nagahama City, Shiga Prefecture
Gifu Castle, Gifu Prefecture,
Sekigahara, Gifu Prefecture
Todaiji Temple (Nara city)
Obitoke-dera Temple (Nara) This is the place where Gou played earnestly for a son. It is located 6 km south of Heijo Palace
Matsuga-shima Castle, Miyagi, Tōhoku region, possibly the same place as Matsushima Miyagi, which is one of the Three Views of Japan.
Gokonomiya Shirne, Fushimi Ward, Kyoto
Fushimi Castle (Kyoto) this is where Senhime was born.
Honnoji Temple (Kyoto)
Daitokuji Temple (Kyoto) Soke-in
Nijo Castle (Kyoto)
Hokoji Temple (Kyoto)
Toyokuni Shrine (Kyoto)
Yogen-in Temple, located in Higashiyama district kyoto city, was established by Yodogimi(or Yodo-dono), concubine and second wife of Toyotomi Hideyoshi, for holding a memorial service for her father Asai Nagamasa. it was destroyed by fire in 1619 and rebuilded by Sugenin, using Fushimi Castle's remains in 1621
36 Peaks of Higashiyama (coast of Kyoto)
Himeji Castle, Hyogo Prefecture (between Osaka and Kyoto). Home of Kuroda Kanbei.
Okayama Castle, Okayama Prefecture.
Construction of Okayama Castle was started in 1573 by Ukita Naoie and completed by his son Hideie in 1597. Three years later, Hideie sided with the ill-fated Toyotomi Clan at the Battle of Sekigahara, was captured by the Tokugawa Clan and exiled to the island prison of Hachijo. The castle and surrounding fiefdoms were given to Kobayakawa Hideaki as spoils of war. Kobayakawa died just two years later without leaving an heir, and the castle (and fiefdom) was given to the Ikeda Clan, who later added Kōraku-en as a private garden.
Mt Chausu, Osaka
Sakai City, Osaka Prefecture
Sankō Shrine (三光神社 Sankō-jinja) Shigino Shrine/Ikutama Shrine, Osaka.
Jokoji Temple, Obama. Jokoji is a famous temple built in Kan'ei Year 7 (1630 AD). In addition to invaluable portraits, handwritten letters, and the grave of the real Joko-in herself, the murals left in her drawing room help us to recall the prosperity of ancient times.
Obama Castle, Fukui Prefecture. In 1601 after receiving Wakasa Province due to successes in the Battle of Sekigahara, Kyōgoku Takatsugu (京極高次) (the husband of O-Hatsu) built Obama Castle by using local fisherman as workers
Nochise Mountain Castle Ruins (near Obama Castle)
Kanazawa, Ishikawa Prefecture. (This was the seat of the Maeda, where Gou’s third daughter, Tama married aged 3)
San'en-zan Zōjō-ji (三縁山増上寺 San'en-zan Zōjō-ji) Tokyo. Six of the 15 Tokugawa shoguns are buried at Zōjō-ji. The Taitoku-in Mausoleum of Hidetada (and the monument to his wife Sūgen'in),
Nikko, Tochigi Prefecture, is where mausoleums of Tokugawa Ieyasu and Iemitsu.
Nikko is also close the Ashikaga Gakko (Tochigi Prefecture), which is Japan’s oldest academic institution. I want to visit this because I have a strong interest in Confucianism in Japan.
Shizuoka Castle, Shizuoka Prefecture
Mt Kuno, Shizuoka Prefecture. There is strawberry picking here apparently.
Sumpu Castle, Shizuoka Prefecture
Atami Hot springs/Onsen, Shizuoka Prefecture (that’s the episode where Hidetada visits the hot springs)
Odawara Castle, Hakone (100 km from Tokyo)
Kenchō-ji (建長寺) is a Rinzai Zen temple in Kamakura, Kanagawa Prefecture. Part of Gou’s mausoleum was moved here from Zojoji Temple.
Shōkozan Tōkei-ji (松岡山東慶寺?), also known as Kakekomi-dera (駆け込み寺?) or Enkiri-dera (縁切り寺?)), is a Buddhist temple and a former nunnery, the only survivor of a network of five nunneries called Amagozan (尼五山?), in the city of Kamakura in Kanagawa Prefecture,
In the summer of 1615 Princess Naa, the granddaughter of Toyotomi Hideyoshi, was brought to Tokeiji convent in Kamakura from Osaka when she was seven years old to save her life. Her father Hideyori and his mother Yodo-gimi had just committed suicide in Osaka castle, and her eight-year-old brother was beheaded. Sen-Hime, who was Naa-hime’s stepmother, pleaded with her grandfather Tokugawa Ieyasu to spare the little girl. Tokeiji was founded as the first convent to be used as a sanctuary for women by Abbess Kakusan after the death of her husband (the 8th Kamakura Regent Hojo Tokimune).
Karatsu Castle and Imari in Saga Prefecture. The ruins of Nagoya Castle (名護屋城 Nagoya-jō in Hizen province) are in Karatsu, this is where Toyotomi Hideyoshi launched his invasion of Korea. Fans of Jingbirok take note.
Mentioned in one of the little documentaries at the end of each Gou: Himetachi no Sengoku episode is Hogenji Temple, a google search reveals there to be two such temples: one in Matsumae-cho in Hokkaido, the other in Miyoshi, Hiroshima. Since none of the characters in Gou go to either of these places, I think I might have misspelt something and it is actually Hozenji Temple in Osaka.