Butch Lesbian: Apart from her hair, Mokou fits this very, very well.
Butt Monkey: Fukakusa. Right after he was introduced, Fuka was attacked by Reimu's Anti-Yukari danmaku, threatened by Momiji, One-shotted by Ranma, and then Shikieiki comes out of nowwhere and starts pulling his ear. All within the span of two minutes.
In the same scene, Elly was caught by Gengetsu in a similar situation, but was released when Chen broke free. Why? Mugetsu let go of Chen.
Dark and Troubled Past: Vaguely hinted at for Yuuka's back story near the beginning. Plus there's the mentions of her being pretty Ax Crazy until she 'settled down' in Gensokyo. Suwako also has hints of this as well, just it's never been brought up.]]
Yuuka's double (Usually summoned when casting Dual Spark) watched Flandre as she was tickled mercilessly in an old torture device lying around Yuuka's basement. While it was only for a few seconds, with no real consequences, the 'original' Yuuka wasn't amused at the inaction, blaming 'Yuuka 2' for Flandre even hiding inside it in the first place, and forced her clone to enter another device that melts bones.
Ghost Amnesia: Yuyuko experienced this upon her death and subverted the trope like in Canon. Panko lost her memory (after being killed as a ghost) and has forgotten so much that she doesn't even understand what food is. After a night of rest though, she recovers
Going Commando: The Cute Unnamed Onryo is this, not actually understanding the concept of undergarments. Panko corrects this.
Immortal Life Is Cheap: With many of the characters being invincible and able to resurrect, this is exploited a lot:
Mokou and Kaguya have died several times each and resurrected. In fact, the mechanics of one of Mokou's spellcards works by repeatedly killing herself.
Komachi has been impaled with her scythe. Being a shinigami, she just didn't die.
Suwako's had internal brain bleeding, has been impaled, and was Twilight Spark'd by Mima. Each time she either simply split herself or healed her wounds
The fairies, oddly are remarkably good at not dying.
Improbably Female Cast: Not only have the male characters merely been referenced—apart from a one-off gag—all the OC's are female, too. Then Averted with the advent of Fukakusa, the (sofar?) only male NPC and then Ecthel, the first Male PC. And now Youki Konpaku has turned up.
Interface Spoiler: During Utsuho's introdution she spoke normally. After she was hit in the head, her speech text turned gold. It's a major hint to her being possessed even for people unfamiliar with Touhou Nekokayou.
Mundane Utility: Reimu can use ofuda as protection from rain when she doesn't have an umbrella.
Nice Job Breaking It, Troll: Yukari's victory over Reimu depowered the shrine maiden. She spent a day recovering, while incident causer was still causing trouble. That was exactly what Yukari was planning, but she endangered the world will her actions.
Nosebleed: After being soaked in water and having her neck snapped, Mokou's sarashi was in considerable disarray. This was the reaction from Kaguya and Shujiko.
Aya had to do something for Rin to borrow her wheelbarrow. All we know is that it's embarrassing and there's pictures of it on Aya's camera.
How in the world did Fukakusa and Aya's Prank War begin?
No-Holds-Barred Beatdown: Natsumi tried issuing one during the final battle, binding everyone and unleashing a holy amount of danmaku. In response, everyone present during the battle are using their strongest cards on a defenceless Natsumi, essentially giving her the beat down.
Onsen Episode: Actually, bath episode: 7 girls gathered to bath together in Yuuka's mansion. With lot of fanservise and girl-on-girl action.
Playboy Bunny: Suwako got Kaguya to dress like this, before Mokou reminded her that one of her Impossible Requests is a piece of clothing.
Polar Opposite Twins: Mugetsu is willing to do anything to 'reclaim' her land from Yuuka's possession, even holding Chen hostage. Gengetsu likes to mess around and fight strong opponents other than Yuuka.
Power Tattoo: Mokou's tattoo, despite being a phoenix and her powers over fire having come from eating one, is actually not one of these.
Smoking Is Cool: Mokou certainly falls under this. It's not as if it can kill her or make her health any worse, though. Kaguya occasionally gets in on it, too, which is behind the Noodle Incident fire in canon.*
Mokou accidentally incinerated Kaguya's head and set the forest on fire when lighting a cigarette.
Stringy-Haired Ghost Girl: The Panko is a Onryo, a vengeful spirit who returns to the mortal world for revenge. This being Gensokyo And her being a Goddess when alive, she's actually subverts the trope and the usualOnryonature. Doesn't stop her desires for revenge though. For at while at least.
Fukakusa may count too: to start a prank in Hakurei shrine, to scare Hot Blooded shrine maiden and then to turn his back to her and drop guard. Even though he couldn't have foreseen Reimu's reaction (due to never meting her) she's a Hakurei shrine maiden, he should of known better.