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Romantic and/or sexual relationships between characters are an extremely popular subject in Touhou doujinshi and fanart. Of course, since almost all of the characters are female, "everyone in Gensokyo is gay" is itself a meme. This is intended to be a list of the couples most commonly seen in fanon and excludes "crack pairings". Brief explanations of likely Canon origins, or at least excuses, are also welcome.

Main Character Harems

As the protagonists, Reimu Hakurei and Marisa Kirisame are frequent subjects of shipping speculation, both with each other and with enemies they've defeated. Marisa, however, is often considered to have a larger "harem".

Reimu and Marisa appear as playable main characters, usually both in the same game, in all Touhou games except Shoot the Bullet. They are also shown to be acquainted in several places in the games, sharing a sort of on-again-off again comraderie. This is a pairing popular with fan authors such as Rocket Fuel 21 and Asian Big Brother Generation, often featuring an affectionate and aggressive Reimu and a bashful Marisa, though other authors have created several other interpretations concerning which party is the dominant in the relationship.
In one of the endings of Embodiment of Scarlet Devil, it is mentioned that Remilia often visits the Hakurei Shrine. Naturally, this was taken further.
Reimu and Yukari- the border's shrine maiden and the youkai of the border- made up the Border Team of Imperishable Night. Their relationship in fanworks is usually identified by Yukari playfully teasing or flirting with Reimu, who often acts irritated or impatient with the advances but may become receptive to them eventually.
With no home to go after the events of Immaterial and Missing Power, Suika was taken in at the Hakurei Shrine. The two must get bored and lonely some days.
Simply comes from the fact that the two are both shrine maidens.
Alice and Marisa make up the Magic Team of Imperishable Night, and as the two are both witches living (presumably) in the same forest, they are often shown to be friends or at least acquaintances. In fanworks the pair is depicted as being somewhat troubled, with Alice hiding her feelings for the often-oblivious(?) Marisa. In some works the anxiety put upon her can become deadly, as she begins to develop obsessive and jealous tendencies that may end up in her harming Marisa or herself. This pairing is popular among fans, bolstered by the popularity of Marisa Stole The Precious Thing and the general bloodthirstiness of the Touhou fandom in general.
One of the endings to Embodiment of Scarlet Devil, plus articles from Perfect Memento in Strict Sense and Bohemian Archive in Japanese Red, all make reference to Marisa stealing books from Patchouli's library in the Scarlet Devil Mansion. It is assumed that there is a reason Patchouli tolerates this. In fanworks, Patchouli is often shown sharing her books reluctantly with Marisa in order to have a reason to spend more time with her.
Upon defeating Flandre in Embodiment of Scarlet Devil, Marisa suggests for Flandre to get married. The assumption is that this was not entirely a joke.
Rinnosuke has known Marisa since she was a child, and the two are occasionally portrayed as harboring affections towards each other.
This pairing was inspired by the option of letting Nitori become Marisa's youkai partner in Subterranean Animism's Marisa type C firing mode.

Masters and Servants

The suffering and frustration experienced by serious-minded servants at the hands of their exasperating, capricious masters is a frequent source of humor in both official works (especially Inaba of the Moon and Inaba of the Earth) and fanworks.

Daiyousei may have authority over Cirno, but she's the one who can get exasperated over Cirno's behavior.
The above is also true for Letty.
In their case, it's Sikieiki who's serious and and Komachi who's the flaky servant.

General Pairings

Keine appears in Imperishable Night's Extra stage to protect Mokou.
Comes from Cirno's ending in PoFV which features her and Aya.
The doll maker and the living doll.
The similarity of Nitori's hairstyle to that of PC-98 character Chiyuri led to jokes about them forming a "Twin-Tail Alliance". Their shared interest in science only furthered their pairing status.
The only two individuals known from the world past Gensokyo's border. In a night-activities club that consists of only them.
Often features the two acting as "parents" for Sanae.

Domination or Rape

As often seen, but may also be depicted in romantic and consensual contexts.

Usually involves Meiling having an unrequited crush on Sakuya, and Sakuya frequently stabbing Meiling in the head for not doing her job as door guard.
An extension of the meme about Yuyuko trying to eat Mystia.
Eirin is frequently shown, even in the canonical Inaba of the Moon and Inaba of the Earth, to subject Reisen to medical experiments and corporal punishment.
Canonically, both of them continually fight each other with deadly force, even though they're immortal and regenerate all damage.
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