Sakuya is unwaveringly, inexplicably subservient to Remilia. There is absolutely no explanation for why a powerful, capable human has devoted herself entirely to a petulant, selfish brat of a vampire, and a Bodyguard Crush is far from implausible.
Youmu exhibits a similar devotion to Yuyuko, constantly acquiescing to the whims of a millennium-old child but never shirking her duty. She was even willing to steal the essence of spring from Gensoukyou and plunge it into eternal winter simply because Yuyuko told her to.
Eirin made an immortality potion - forbidden by law and punishable by exile - just because Kaguya asked her to. When sent to retrieve Kaguya from Earth once the latter's exile is deemed over, Eirin instead betrayed and killed her entourage, exiling herself from her home and her position as "brain of the moon" so she could be with Kaguya. She even hides most of her power so that Kaguya isn't offended by a subordinate with more power than her, something completely unprecedented in Touhou, and even more significant after ZUN stated in Symposium of Post-Mysticism that Eirin is one of the ultra-powerful gods of the moon.
Mokou harbors a literally eternal hatred towards Kaguya for an "offense" made against her father centuries ago, which combined with Kaguya viewing their "rivalry" with more amusement than anything else makes Mokou seem more like a gigantic Tsundere.
The semi-canonical Inaba of the Moon and Earth only seems to confirm what a Tsundere Mokou is, though as a Gag Series it naturally plays fast and loose with characterisation to begin with.
Meanwhile, Mokou has been living as a hermit and vagrant for centuries, isolating herself from others because she can't bear to see them die while she never changes... except for Keine, who is literally Mokou's only friend and even tries to protect her. Mokou knows what will happen, but can't quite bring herself to avoid Keine as she does with everyone else.
Suika lived with Reimu for a while after defeating her, though Reimu is mostly annoyed at Suika mooching off of her.
Yukari teases Reimu relentlessly, alternating between Trickster Mentor and this trope.
In Marisa's route against Flandre in the EoSD Extra Stage, she makes a comment about hooking up Flandre with Reimu.
Reimu seems to be a youkai magnet. Mima was pretty much obsessed with her, Remilia apparently goes periodically to Hakurei Shrine just for taking tea, and Rin wanted to be her pet. And after every game, no matter how much pride has been crushed and bullets have been fired into faces, everyone always go to Reimu's party for tea and giggles.
Reimu is known for being equally irreverent and brutally frank with everyone she knows, human, youkai, or goddess. The only exception to this rule is the little bookworm Kosuzu, whom she even has a pet name for!
Marisa and Alice... there is a reason these two are the single most popular pairing in the fandom. Ever since they met (again?) in Perfect Cherry Blossom they have formed a bizarre partnership unique to Gensoukyou based not on greater power or authority but lots and lots of snark, spending almost the entirety of both Imperishable Night and Subterranean Animism arguing Like an Old Married Couple, often ignoring the boss just to trade snipes. And yet, they still hold a large amount of affection for each other, Alice abrasive and rude towards everyone but displaying a rare sentimental side with Marisa, while Marisa herself, though very much a Jerk with a Heart of Jerk, is far more respectful towards Alice than she is to anyone since Mima. And they even share a bed in one of IN's Bad Ends.
The always unclear and widely speculated relationship between Marisa and Mima tends to vary from master and servant, to mother and daughter, to even something romantic. It doesn't help that Marisa's profile in Phantasmagoria of Dim. Dream states that she longs for Mima and calls her with the extremely respectful honorific -sama (making Mima the only person in the entire series to whom Marisa is ever polite and respectful towards).
Yuyuko and Yukari, close friends for more than a millennium, even before Yuyuko died. Yuyuko's Perfect Cherry Blossom profile heavily hints it was Yukari who ensured that she would never resurrect and continue existing as a Cute Ghost Girl, with one line suggesting that it's one-sided.
"My wish... is that she will never again reincarnate, and never again suffer pain..."
Kanako and Suwako from Mountain of Faith: they first met when Kanako declared war on Suwako's followers and won, and since then they've been living together for about half a millennium, and they raised Sanae together. Not bad for two people who started as enemies...
Also worth mentioning the fact that Kanako's character is apparently based off the actual Shinto goddess Princess Yasakatome, who lives in the Suwa Taisha shrine. With another deity: her husband.
Byakuren and almost the entire cast of Undefined Fantastic Object, all literally worshipful of and intensely loyal towards Youkai Jesus.
The fan-game Concealed the Conclusion is basically a Rescue Romance, with Marisa being warned in no uncertain terms by nearly everyone in Gensoukyou to stay away from Reimu and just let her go, Marisa pressing on regardless and eventually leading to the the final, emotional confrontation with Reimu herself. And Scenario D even manages to add some Marisa/Alice hints, with Alice adding "why don't you stay with me?" to her "let Reimu go" speech.
Speaking of fangames, Touhou Mother makes Marisa into a complete Chick Magnet without letting that override the plot. The ressurected Mima, despite mocking Marisa for it, is no slouch in this department herself, openly flirting with Yuugi Hoshiguma and getting awkwardly proposed to on sight by Satori Komeiji of all people.
Soga no Tojiko is based off of Tojiko no Iratsume. Toyosatomimi no Miko is a genderbent Prince Shoutoku. Historically, Tojiko no Iratsume and Prince Shoutoku were married.
Some of the pre-battle dialogue with bosses can sound pretty flirty, such as this from the Embodiment of Scarlet Devil (Patchouli's presumably talking about literally eating her - Patchy is a youkai - but it can certainly be taken the other way):
Marisa: I have enough. Of plenty of things.
Patchouli: Then I'll dig in.
Marisa: I'm really delicious.
In Story of Eastern Wonderland, Reimu mistakes Meira's challenge for a marriage proposal, and accepts on the spot. She gets annoyed when Meira tries to clarify things.
Meira: I am Meira. I have come to take the Hakurei (powers).
Forbidden Scrollery has Kosuzu being rather... taken... by Mamizou's human guise, practically crushing hard over the tanuki-pretending-to-be-human, and squeeing over the interesting books and recommendations she gets. Is Reimu disapproving of Mamizou because of her Tanuki machinations, or is it because she's jealous that Kosuzu shows so much interest in the Tanuki?
In another angle, Kosuzu is very close to Akyuu. Close enough to show her hidden side of cynicism and engage in banter even Reimu never gets to partake in. Their friendly rivalry as fellow bookworms might hint at something more.