Disclaimer: I don't own Touhou Project and its locations.
Aki Supēsu: Is a desolate wasteland with a black sky and white sand. This place is mostly inhabited by several void creatures and familiars. The realm is where Kyomu lived here, which means she is the creator of this place.
Scarlet Devil Mansion: This western style mansion is the home of its mistress, Remilia Scarlet. It's staff consists mostly of fairy maids, though they do a horrible job at cleaning maintaining the mansion so its head maid, Sakuya maintains the place all by herself. Flandre Scarlet also resides in the mansion, but originally lived in the basement up until the Scarlet Mist incident, which led to her being let out of the basement more often than usual. The mansion's library, Voile, is occupied by Remilia's friend Patchouli with her familiar Koakuma and Tokiko. The gatekeeper of the SDM is Hong Meiling, and she also maintains the mansion's beautiful garden.
Netherworld: This realm is where souls judged by Yama to be guiltless go to as phantoms to achieve nirvana, or reincarnate. Beautiful Cherry blossoms in the realm are seen throughout it as well. Originally barrier of Life & Death prevented, the inhabitants of Gensokyo to enter the Netherworld, because it was a distinct part of Gensokyo. However during the Spring Snow Incident the barrier was weakened by Yuyuko, which made it easier for Gensokyians to fly over and enter the Netherworld. After the incident, Yukari Yakumo was supposed to fix the boundary, but never bothered to do it.
Hakugyokurou: Is a ghost shrine, located in the realm of the Netherworld. The owner of the place is Yuyuko Saigyouji, and the gardener was Youmu Konpaku. The Sagyou Ayakash, a youkai tree, is dormant and resides in the gardens of Hakugyokurou.
Eientai: This old fashioned Japanese styled Mansion is where the two Lunarian exiles, Kaguya Houraisan and Eirin Yagokoro live in. The place is also occupied by a lot of rabbits along with Tewi Inaba, Reisen Udogein Inaba, and Rin Satsuki who all protect Eientai from intruders. After the Eternal Night Incident Eientai served as the only medical place in Gensokyo where both youkai and humans can get medical services from Eirin.
Crypt of Alexandria: Is a small Egyptian pyramid owned by Masud Akh. The pyramid was created by Masud to be his place of residence. Recently it got new inhabitants who are Medusa, Jack, and Catori Valencia. The Crypt has several flying talimans that allow it to fly in the sky. Its also has a huge teleportation talisman that Masud installed in the crypt.
The Underworld: Is a world that consists of several regions below Gensokyo. The highest region was Former Hell, and below that was the Remains of Blazing Hell. The Former Capital, and the Palace of the Earth Spirits are located in Former Hell.
Sub locations:
Former hell: Is formerly Gensokyo's hell where sinners and people who committed heinous crimes go to. However hell was moved by Hecatia to a new spot, because most of the suns in that hellish place were shot down by Houyi. The place where Gensokyo's once was at is now, Hecatia gave the place to Satori to both keep the vengeful spirits from leaving, and also for both youkai and humans to not bother her.
The Former Capital: Is a large traditional Japanese styled village located in Former Hell. The place is primarily inhabited by Oni, because they were allowed to stay there by the Yama and Hecatia. Yuugi, one of the Deva of the Mountains, resides here in the Former Capital throwing parties and drinking with her fellow onis.
Palace of the Earth Spirits: Is a western-style mansion, which is located in Former Hell. The mansion is inhabited by Satori and Koishi Komeiji, along with their pets. Satori is the owner of the mansion and is maintained by her pets.
Remains of Blazing Hell: Was originally where criminals were sent to be burned in hellfire, but was cooled down. It was later reignited, after the Nuclear Furnace was activated.
The Nuclear Furnace: Is a super-high furnace that is capable of producing nuclear fusion power. The Furnace is maintained by Utsuho Reiuji, and is kept running by Orin chucking corpses into it. Kanako Yasaka and Suwako Moriya wanted to use the furnace to revolutionize the kappa's energy production during their Mountain Industrial Revolution project.
The Palanquin Ship/Myouren Temple: The Palanquin ship was created by Byakuren given to Murasa to free gain her trust. It was based on the same ship that Murasa died on. Murasa is the captain of the ship, also housed Byakuren's youkai members, Shou, Unzan, Ichirin, and Nazrin.
After Byakuren was sealed the ship ended up being buried in the Underworld for a while until the Subterranean Incident occurred. During the incident the geyser caused by Orin ejected the Palanquin ship and its crew from the ground and into the air. When the UFO incident occurred, Byakuren's group of youkai flew to Makai to go rescue the Buddhist monk.
After the UFO incident Byakuren had the ship transform into the Myouren temple and be intentionally placed on top of the Hall Dreams' Great Mausoleum to prevent Toysatomimi no Miko's resurrection from happening. Although in the Ten Desires Incident, Miko's resurrection still occurred, because the divine spirits of Gensokyo were attracted to it. The Myouren Temple nowadays serves as a place to worship Buddhism, and also to help promote youkai and human peace.
The Hakurei Shrine: Is a shrine that lies in the Great Hakurei Barrier separating Gensokyo from the Outside World. Despite its importance to Gensokyo, it rarely gets human visitors, and even rarer donations. The only visitors that the shrine gets is the various sorts of youkai that come to the shrine that the Hakurei miko has defeated in the past. The current Hakurei miko is Reimu, and she is usually called to resolve incidents that plague Gensokyo. Originally the Hakurei Shrine was the only shrine in the land of illusions, but the Moriya Shrine has settled in the Youkai Mountain.
The shrine had a god known simply as the Hakurei God, but it wasn't revealed who he or she was until the Dragon Incident, where it's revealed that it was Annaya Hakurei. Recently the Hakurei Shrine had a bigger influx of followers than it had before, who were both youkai and humans, after the Dragon Incident. This is because the path to the Hakurei Shrine was easier to navigate, because of Ryūjin's help. Another reason for its popularity is because the Dragon God usually hangs out at the shrine, which led to a lot of people coming to visit and more donations being given to Reimu's donation box. This meant the Hakurei Shrine can now rival the Moriya Shrine in terms of followers and faith.
Youkai Mountain: Is a huge mountain covered mostly by the Great Youkai Forest at its foot, with several waterfalls and rivers flowing from the lakes at the mountain top. This place serves as the home of the Tengu and Kappa, whom the former has authority over the latter. Any outsider who trespasses on the mountain will be chased out by the Tengu's patrols.
Before the Tengu took over the mountain they and the kappa were originally ruled by the Oni and their leaders the Four Devas of the mountain. However, after the Hakurei Barrier was created the oni and their leaders left the mountain, because things have gotten uneventful.
Sub locations:
The Great Youkai Forest: is a great forest that is located at the foot of the youkai mountain.
The Genbu Ravine: Is a ravine where some of the kappa live at.
The Untrodden Valley: is a valley located at the very bottom of the the mountain which has a river from one of the many waterfalls that courses through it. This place is also where the kappa village is at.
The Kappa Village: Is the place where most of the kappa live in. Unlike most places in Gensokyo it resembles a modern city from the Outside World. It also worth to note that that the Probability Space Hypervessel is rests here.
The Tengu Village: Is where most of the tengu's population is currently located in. Like the kappa village the place is also technological advance in the form of factories that produce newspapers and other publications. Lord Temna lives in this village governing all of the tengu of the mountain.
Moriya Ropeway: Is an aerial transport constructed in the year 2017. It was finally allowed to be constructed after Kanako managed to get the Tengu to agree to constructing it.
It allows non flying humans to be able to access the mountain easier.
The Moriya Shrine: Is a Shinto Shrine that is located on the Youkai Mountain. The local shrine maiden of the place is Sanae Kochiya, and its residents goddesses are Suwako Moriya and Kanako Yasaka. The shrine was moved into Gensokyo, because of the lack of faith in the Outside World.
The Moriya Shrine tried to shut down the Hakurei Shrine in order to get more faith, but this ended up causing the Faith Incident. After the incident the Moriya shrine, and Hakurei Shrine are still rivals even if the latter has a lack of followers and is very poor.