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Danganronpa: Trigger Happy Havoc

Let's start with Chapter 1.
- The first victim is Sayaka, who's opted to take shelter in Naegi's room for safety the night before.
- A few moments later, Junko is killed for attacking Monokuma, in a grim showcase that Anyone Can Die in this killing game.
Then at the end of Chapter 2, it's revealed there is a mole among the students, and there's also a separate sixteenth student that Monokuma is hiding.
After the fourth trial is ruled a suicide, Monokuma declares that he won't let his execution go to waste and will punish a "special guest". Makoto wonders who said guest could be... when suddenly the screen cuts to a close-up of Alter Ego's face, causing a massive Oh, Crap! in the students (and likely the player) as they realize Monokuma's about to crush what seems like their only chance of escape at the time.
During Makoto's "execution", Alter Ego appears on the monitor, turning out to be Not Quite Dead. The execution is sabotaged and Makoto gets to escape.

Danganronpa 2: Goodbye Despair

During the Chapter 1 class trial, Hajime and Chiaki identify the culprit that planted the knife under the table and went to grab it during the power outage. When the culprit is cornered, they're left chuckling as a distraught Hajime asks him to object or refute the allegations, but what follows is one laugh and a chilling line that establishes Nagito's true nature:
Nagito: Ahahahahahahahahahahahahahahahahahahahaha! The Ultimates are working together to combat the despair of their friend's death! Ah, how wonderful, how beautiful it is!

Danganronpa 3: The End of Hope's Peak High School

Future Arc

At the end of Episode 2, after the sleeping drug knocks everyone out and the attacker strikes, Makoto awakens and finds Aoi seemingly stabbed in the stomach. It was actually fake.
Episode 4 ends with a shot of Monaca Towa controlling a robot Gekkogahara, dressed up in her Junko-esque outfit from the end of Danganronpa Another Episode: Ultra Despair Girls.
Episode 6 ends with Munakata's peacekeeping forces heading to Jabberwock island, with someone who looks like Hajime watching them from a dock. The final shot has a closeup of his eye, which opens to reveal a red pupil as he says "This is so boring."
Episode 8 ends with Byakuya's team accidentally triggering a bomb inside the Future Foundation base, causing the building to start sinking.
At the end of Episode 9, when everyone awakens, they discover Kyoko has died due to her forbidden action.
The end of Episode 11 shows Ryota's cell phone with a text from the thought-to-be deceased Tengan.

Despair Arc

At the end of Episode 10, the camera pans up to show Izuru crying over Chiaki's death, with the next episode confirming this is what turned him against Junko.

Danganronpa V3: Killing Harmony

Shuichi demands to know the real identity of the Mastermind, and he gets it:
Shuichi: So who the hell are you!?
Tsumugi: (turns into Hajime Hinata) I'm me. No one else.
The turning point of Chapter 6 shows who this killing game has been broadcast to: A massive audience, all in the outside world, watching the students kill each other for their entertainment.
In the lead-up to the final Voting Time, where Shuichi, Himiko, and Maki have chosen to abstain to create an anticlimactic end to the killing game, Tsumugi reveals she's also abstaining so that Kibo's remaining vote (reflecting the audience's will) becomes the sole deciding factor of the outcome. Cut to the vote screen that displays a "No Votes" alert, revealing that Shuichi has successfully convinced the audience to move on from the killing games.

Killer Killer

Two in Chapter 3:
- When Hijirihara kills Saiyama, the background shifts to depict Monokuma, confirming this is indeed a part of the franchise.
- Subverted with the ending. Asano sees what seems to be Makoto Naegi's corpse, only for the following chapter to out it as firework.
In chapter 4, Chikatilo walking into the stadium midway through the fight between his doppelganger and Hijirihara. This is followed by outing the imposter as Juuzou Sakakura.
Chapter 8 has the lovely image of Mukuro Ikusaba cutting her way through a middle school.
Chapter 9 has a pretty big one. Fujigawa stabs Asano through the stomach.
Chapter 10 features one with the appearances of Sonosuke Izayoi and Ruruka Andou.
Chapter 12 has an appearance from Kazuo Tengan, who plants a tracking device/detonator on Asano.

Wham Shot / Danganronpa