Each time Naegi figures out the culprit and how the crime occurred, right down to every last minute detail.
Especially when Naegi finally figures out, in chapter 6, who the mastermind behind this whole fiasco is. Made even better in that Naegi's chain of reasoning began because he noticed something as small as there being only 9 indicator lights in the morgue instead of 10!
Oowada and Fujisaki symbolically lending their aid from beyond the grave. Oowada's spirit fuses with Kiyotaka, and Fujisaki leaves behind Alter Ego, a program that can help connect with the outside world.
Oowada's reaction to his execution, being tied to a motorcycle and sent into a "death cage". Unlike Kuwata, he doesn't struggle or attempt to escape the motorcycle in any way, accepting his punishment for killing Fujisaki.
Asahina slapping Togami across the face for being such a Jerkass.
After the fourth trial, everyone (even Togami and Fukawa, in their own way) stand up and tell Monokuma they're done playing his game, and that they'll be working together to take down him and the mastermind.
Sakura Oogami gets a post-mortem crowning moment of awesome when it's revealed what her "first shot" against Monokuma was: Oogami broke the lock to an important door Monokuma was guarding so Kyouko Kirigiri could break in and see what was inside.
The true ending of Chapter 5. Naegi's about to be crushed to death for a murder he didn't commit, when...surprise! Alter Ego turns out to have uploaded a virus to the school's network! The virus stops the machine and opens a trapdoor under Naegi's feet, robbing the piston of its intended victim, just in time, much to everyone else's shock!
Naegi mirroring Kirigiri's reaction to it is impressive, when you think about it. The player's first assumption would probably be that he'd freak out.
The best part of the whole scene? Monokuma's little Villainous Breakdown right after Alter Ego's rescue. After spending so much time looking down at the students, laughing at and blaming them for descending into despair, he's finally getting a taste of his own medicine. And you can just tell that it tastes bitter. So. Very. Bitter.
Bonus: Fujisaki wanted to be strong. Alter Ego, essentially a digital copy of Fujisaki's personality, has become strong enough to hold back a killing machine.
Chapter 6. Naegi helping everyone overcome despair and earning the title of SHSL Hope, and then using that hope to deliver the final blow to the mastermind. The Last Episode Theme Reprise definitely warrants a mention, too. And on a meta level, Naegi finding the seeds of hope in the words of the mastermind.
There are quite a few of these in Dangan Ronpa IF, including Mukuro Ikusaba being able to match fists with Sakura Oogami, Ikusaba fending off hundreds of Monokuma units, Oowada and Oogami saving Mukuro from said units (including Oowada riding the motorcycle used in his execution), and Ikusaba's gambit to get through the Final Graduation Exam.
For the anime: The Reveal of the Mastermind's identity. Not being limited by sprites limitations is a good thing.
Also, Naegi going more than "You must not lose hope!" to instill hope in his friends, he frigging tailored A LOT of Rousing Speech to raise their spirits and it works!
Celeste's English VA during her Villainous Breakdown; she's had a subtle French accent throughout the game, but as she loses her composure, she perfectly nails it falling apart, from growing hilariously extreme to suddenly going to a more American one like the other characters when she's screaming at people.
Usami's Early-Bird Cameo in Dangan Ronpa's School Mode, beating down Monokuma when he is about to execute Naegi and forcing him to give up the escape switch to let them escape the school.