Art Evolution: The drawing improves with each episode, going from the very rough style of the first episodes, to a much more smoother style by the time of episode 7. Episodes 11, 12 and the first part of 13 are in Deliberately Monochrome, with the occasional Splash of Color.
Beware the Nice Ones: Aside from those already driven crazy, Kogasa goes from cute, assuming youkai, to saving herself from Sanae's Cold-Blooded Torture via umbrella impalement, all while crucified. It's clearly desperate self-defense rather than Unstoppable Rage, but the way she gives her trademark tongue expression and chants 'Urameshiya' beforehand is....
Big Bad: Koakuma is revealed to be the reason why everyone in Gensokyo is going bat-shit crazy. Except not exactly.
Big Bad Duumvirate: It appears that Koakuma and Reisen II are this. Reisen II is acting on behalf of the Watatsuki sisters, the actual Duumvirate to Koakuma.
Big Bad Ensemble: The series hints at someone from the moon behind Reisen II's involvement, later revealed to be the Watatsuki sisters who are also the masterminds behind the whole plot, and we still don't know if Byakuren's invasion is from induced madness or not.
Big Damn Heroes: Marisa and Alice show up in the nick of time to prevent Nitori from being burned at the stake by a turned crazy Hina.
Reisen coming out of nowhere to render Reisen II unconscious before the latter can shoot Reimu.
Kanako also performed this awesomely for Sanae to prevent an imminent rape by her bullies.
In episode 12, Marisa and Alice again saving the Human Village from Mokou's rampage, then later Mamizou saving in extremis Alice from Nue while Miko and her group saves Marisa from Byakuren's fleet.
To put this in perspective, the first real fight in the series is when Meiling prevents Koishi from entering the Scarlet Devil Mansion. She gets the entire front of her neck torn out so that the spine is visible.
Sanae captures and tortures Kogasa, before getting killed herself by impalement via the latter's umbrella.
Mokou destroys the human village, and kills everyone in it.
Yuuka does...something unspecified to Medicine Melancholy.
Star Sapphire literally pulps the other two fairies with a chainsaw.
Tewi breaks Reisen's legs with a mochi-pounding mallet.
Satori decapitates Rin with her bare hands...while being carried to safety.
Reisen II kills Yukari by detonating a bomb implanted inside Ran's stomach, then emptying her rifle ammo on her, then by detonatinganotherbomb implanted inside Chen's stomach.
Blue and Orange Morality: Calling Koishi outright evil is a stretch, but she's definitely not playing by anyone else's sense of morality. She apparently gets better after assimilating Yukari's head.
Driven to Madness: The driving plot of the whole thing: SOMEONE is trying to drive all of Gensokyo crazy...and doing a damn fine job too. It's revealed to be the doing of the Watatsuki sisters, with the help of Koakuma and Satori. (albeit begrudgingly for the latter)
Femme Fatalons: Koishi has hands with very long, claw-like fingers. Their exact length tends to change, though.
Fingore: When Koishi gets locked up in a room, she tries to literally claw at the door until all her nails are BARELY attached to her fingers. Then when the story comes back to her again, we find that all her nails have fallen off. Squicky indeed.
Gambit Pileup: The plot is starting to look a little something like this. The three players so far are the Watatsuki sisters, the masterminds behind everything, Satori who's forced to work for the sisters and desperately tries to double-cross them, and the remaining sane people of Gensokyo trying to understand what the hell is happening and stop it.
Late-Arrival Spoiler: There has been many fanarts depicting the most important twists of the story including Koakuma turning out to be evil, Koishi's supposed death and her double resurrection-fusion with Yukari who also supposedly died, and Reisen's seemingly Deadex Machina. Lately also started to appear fanarts depicting the Watatsuki sisters alongside Koakuma and Reisen II, revealing their heavy involvement in the events of the story.
Mercy Kill: A tired and emotionally distressed Satori does this to Orin.
Iku presumably got one from Tenshi.
Mind Screw: It's not clear which parts of the events depicted between Daiyousei and Cirno the night the mass-insanity began are real or a product of them being affected by the madness plague.
Mind Screwdriver: The first part of episode 11 explains a lot of the previous events, give us a Team Shot revealing who hasn't gone crazy and are fighting to resolve the incident, and gives concrete hints about the responsible behind the Hate Plague.
Perhaps Tewi didn't actually crush the real Reisen's legs?
Exactly how canon that part was seems to be debatable, because at the same time, Yuuka was seen seriously injuring Medicine. Yuuka later appears in an image along with the heroes, as someone trying to keep the peace. It could be though that Medicine was just as evil as everyone else.
Oh Crap: A Villainous example, Hina has this moment when she notices one of Alice's explosive dolls just next to her about to explode.
Later, Yukari has one just before a Ran that was turned into a human bomb explodes right in front of her.
Poor Communication Kills: Remilia, toward Flan. Remilia was not there to save Meiling or Flan from Koishi's rampage, because she was at Reimu's discussing Flan's improvement and showing the parasol she had planned to give Flan when she returned to the mansion. As a result, Flan believes Remi only sees her as a burden, which is why she wasn't saved.
Patchouli: You really don't know how to talk to her, do you?
Power Copying: Koakuma's power is apparently the ability to steal powers from the dead, implied by her use of a 'miracle' after Sanae's death. Confirmed after using Sunny's, Luna's, Mystia's, Youmu's, Cirno's and Iku's own powers to fight Reimu.
Puppeteer Parasite: Satori and Koishi, apparently a common trait of their species. Their true body is actually their Third Eye. At least they are considerate enough to only take control of hosts that are already dead.
Red Herring: Played with: Everything points toward Koishi being the cause of everyone turning mad in Gensokyo due to her ability to manipulate the subconscious mind, prompting Yukari to hunt her down and kill her. Turns out not only she's not the cause of the mass insanity, but she was deliberately set up as this trope to make Yukari fall into an ambush set by Reisen II and kill her.
A possibly subtle one: in part 8 Yukari says that her heart is "Far, far in the past", which might be a reference to the fan theory that Yukari is a much older Maribel Hearn that was Trapped in the Past.
Episode 9's head assimilation scene with Koishi's body fusing with Yukari's head is a possible reference to JoJo's Bizarre Adventure at the end of Part 1: Phantom Blood where Dio attempts to assimilate Jonathan Joestar's body as his own. And just like Dio, it is successful.
The art style of the entire series is a Shout-Out to the Dario Argento film Deep Red or more specifically the wall drawing that Carlo drew of his deranged mother stabbing his father after the latter tried to take her to the clinic for her mental instability while lullaby music was playing on a record player,which the killer also needs to listen to in order for her to be able to kill someone by putting herself in the same state of mind as when she killed her husband. In addition,Episode 5 opens with a Nightmare Fuel Coloring Book while the same lullaby (School At Night Lullaby) plays.
Sociopathic Hero: Marisa is a borderline one, not feeling a single shred of emotion at seeing the cadaver of her father. She states that all the time she spent isolated in the Forest of Magic to study magic killed her capacity to feel emotions. What prevents her for being a full sociopath is that she states that there are other people that she did bonded with and come to care for, Reimu and Alice. Worse, even though she makes a grave for her father, she states that it was only because she read a book where the heroine did it, and follows by considering herself the Evil-fighting heroine of a book like in the one she read and start following through the tropes inherent of this kind of story, notably being protected by Plot Armor. There's clearly something not right in her head!
Part 8. Showdown between Koishi and Yukari Yakumo. What song gets played over it? Renai Circulation.
Earlier, Carl Douglas' Kung Fu Fighting is played over a scene where Byakuren Hijiri is inciting a crowd of youkai to kill all the humans in Gensokyo.
Let's not forget the Umineko theme in part 9, which is usually played at banquets or when someone is watching the shoreline. This is played while fighting Reisen II.
Super Mode: Koishi and Satori have one letting them use their Combat Tentacles to near Lovecraftian levels as well as increasing their psychic powers. It manifests by their Third Eye merging inside their body and their left eye changing color (red for Koishi, black with a green slitted pupil for Satori) with a completely bloodshot sclera.
Talkative Loon: Koishi will talk to anyone and anything, including her hat, any one of her replacement hats, and a door.
Reisen implies to be one when she incapacitate Reisen II.
Reisen: Don't worry, I'm very good with captives. In fact, you could even say that's I'm eager to beat the info out of her.
Unwitting Pawn: Strangely enough, the deeper the series goes, the more it seems Koishi herself is one of these. Turns out that she was an unwitting decoy used by the Watatsuki sisters to attract Yukari and have her assassinated in an ambush.
Wham Episode: Parts 8 and 9: most of Gensyoko descent into complete madness, Mokou continue her rampage against the Human Village and horribly wounds Keine, Byakuren gather a large fleet and Youkai army to wipe out all of the remaining humans, Koakuma reveals to have been Evil All Along, Satori murders Orin, Yukari is killed by Reisen II and Koishi turns out not being dead and assimilates Yukari's remains, regaining a functional body and possibly part of Yukari's powers, and is free to continue to wreck havoc. Part 8 even has a disclaimer that it's the most violent and horrible episode to date!
Why Am I Ticking?: A strange and horrifying variation: 1) They're fuse lit bombs. 2) They're sown into the stomachs of the victims. 3) The living bombs are fully aware of it.