One of her magazines covers reads the phase "Monokuro de Kawaii", and yet another has a title beginning with "Twin." Makoto also comments that Junko doesn't quite look like her photos, which Junko attributes to Photoshop.
On that topic, one of her sprites has her fiddling with one of her ponytails with an annoyed face. After all, Mukuro is not used to having such long hair. In addition, she is one of the few characters in the game who lacks Expressive Hair when shocked, angry or scared, which makes sense since her hair is just a wig.
"Junko"'s dying words are "This wasn't... supposed to... Why... me?" This itself doesn't seem to make any sense; Junko just attacked Monokuma, who had earlier proven that he responds to such things with disproportionate violence (and although Mondo, the first to attack Monokuma, survived, Monokuma made it clear that it was the students' one and only warning). It does make sense when you realize 'Junko' is Monokuma's accomplice- Mukuro is utterly shocked that Junko would not only kill her own sister, but that she'd kill someone who was on her side and carrying out her plans.
While a first-time player is unlikely to even try them, many of her favorite free time presents are combat-related like the Muramasa sword and God of War Charm, and the military Ration is even one of her "optimal" gifts.
During their first conversation, Chihiro tells Makoto that he has a feeling that they've met before. Even though Makoto has never met any of his classmates before he arrived at Hope's Peak with the exception of Sayaka, Chihiro turns out to be right since all of the students met two years prior to the events of the game and their memory was wiped.
A minor one when Makoto and Sayaka swap rooms. He informs her of the bathroom door being stuck and reminds her that water is shut off during nighttime, to which she responds that she'll make sure to remember when she uses the shower in the morning. Notice how she says that she is going to use the shower, not take a shower, hinting at her planning to murder someone and pin the crime on Makoto.
Kyoko's inquiry to Monokuma at the end of Chapter 3: "What have you done with my body?" She, much like the near rest of her classmates, is missing two years' worth of memories, so she has reasonably grown quite a bit and doesn't remember it.
Chihiro being a boy is foreshadowed in multiple occasions. He often goes quiet when people point out the differences between men and women, hinting at his inferiority complex, he has no problem hanging out with his male classmates but is not comfortable around the females, his bedroom features a bed with blue sheets when the rest of the girls have pink sheets, and most importantly, Hina and Sakura are confused as to why Chihiro would refuse to train them with in the locker room if "she" wanted to get stronger, with the reason being that he cannot enter the girls' locker room because he's male. Additionally, one of the gifts he likes the most is a perfume that is intended for men to attract women (with the only other male student who likes it the most being Leon, albeit that two girls- Kyoko and Sakura- both at least like it), and gifts he particularly dislikes include feminine things.
Hifumi names "Yasuhiro" as the one who fatally injured him, referring to Taeko Yasuhiro (who goes by Celestia Ludenberg to the others) rather than Yasuhiro Hagakure, but there's no plausible way for him to have learned that "Yasuhiro" is Celeste's real last name (given her extreme reaction to the possibility of it being brought up at the class trial, there's no way she'd tell him), at least within the killing game. He also directly states that he had already met everyone before the beginning of the killing game, but this is dismissed as a delusion caused by head trauma.
Monokuma in the beginning comments that girls can be killed with sharp objects and boys with blunt ones. All the students that were murdered followed this formula: Sayaka was stabbed in the abdomen with a knife and Mukuro was impaled with spears all over her body, whereas Chihiro, Hifumi and Taka were bludgeoned on the head, the former with a dumbell and the latter two with hammers.
It even winds up setting up the reveal that Chihiro is a boy due to him being hit on the head with a dumbell.
Sakura was not killed by a sharp object ... because she committed suicide and was thus not murdered.
At the beginning of chapter 4, Yasuhiro had made a prediction on how no more murders would occur at the school. Yasuhiro only has a 30% chance of being right on his predictions, so one wouldn't think much of it, but he turns out to be right: There are more deaths in the school, but none of them are murders (Sakura committed suicide, Mukuro was already dead all the way back in chapter 1, and Junko executed herself after losing the final trial).
During their first Free Time Event, Yasuhiro tells Makoto that he made a predicition in which they would both have children with the same woman. In the Downer Ending of the game Kyoko is executed for a crime she did not commit and Toko dies of unspecified circumstances, so Yasuhiro, Byakuya and Makoto have children with Hina.
In one of the Monokuma Theaters in Chapter 2, Monokuma states that he can't help but stare when he sees pretty girls. And then ends it with that he stared at a mirror. At first it might seem like the usual Monokuma Theater nonsense, but it takes on a whole another meaning once the Mastermind, Junko Enoshima (AKA The Ultimate Fashionista) is revealed.
Then the next one talks about the difference between killing someone ("Oops! I killed him!") and murdering someone ("Yeah, that's right. I killed him"). Fittingly enough, the second murder is the result of an outburst of rage with no planning involved, and the killer greatly regrets it after the fact.
When the students are preparing to head to the third trial, Monokuma shows up with a duplicate of himself and tries to get the students to guess which one is the real one. At the time, it seems like one of Monokuma's usual jokes to mess with the students, but in reality, he is hinting that there were actually two killers involved and the students have to figure out the "real" one, i.e. the one who masterminded the case.
In Sakura's second free time event, she'll reveal that she is the latest heir to her family's 300-year old dojo and that it's very important to her. Monokuma gets her to (initially) turn traitor by threatening said dojo.
In the fourth chapter, during the third free time slot, you can find Sakura alone in the chem lab, standing next to chemical closet A. She mutters to herself that she's not ready to open up yet, and if you try to hang out with her, she explicitly asks Makoto if he's willing to stand by her but won't initiate a Free Time Event. As it turns out, she later commits suicide with poison found in closet C because even if Makoto and Hina will stand by her, the others likely won't ever again, and during the investigation Hina swaps it with a protein can she took from closet A.
During the Chapter 4 class trial, Genocide Jack curses her bad luck because Sakura should've easily defended herself when Genocide Jack panicked and swung a bottle at her. It's an odd thing to say, considering that Genocide Jack and Sakura supposedly hadn't known each other before the killing game, and definitely hadn't sparred against each other during this time.
An early-game blackboard says it belongs to a "secret beauty". Initially reads like typical blackboard nonsense... except that very accurately describes Junko's takeover and current situation.
At one point, Monokuma mentions having been hibernating for two years, well before you learn why that's a relevant length of time.
Monokuma also jokes about not giving his three sizes. This is actually a clue that the Mastermind is a girl since this is not something that a guy would bring up.
During the first trial, Celeste asks Monokuma why the court room has sixteen stands if there were only fifteen students trapped at school. Monokuma simply says that the room was built with sixteen people in mind and that there's no further meaning to it. At the end of chapter 2 however, Monokuma admits to a student that there is a sixteenth student at school, but refuses to reveal their identity. It's eventually revealed that the mysterious sixteenth student is Junko's twin sister Mukuro, who got killed all the way in chapter 1 while she was disguised as Junko, and her body was reused to stage the fifth trial. In the final class trial Monokuma takes the empty sixteenth podium, and so does Junko when she reveals her true identity.
Danganronpa: The Animation:
When Sayaka reintroduces herself to Makoto during Episode 1, Junko can clearly be seen behind her, fiddling with one of her pigtails with an odd expression. It's because she's actually Mukuro, and not used to having such long hair.
In Episode 4, Chihiro is seen programming something in his room. This would later be revealed as Alter Ego, but by the computer is a tool kit, something only meant given to the boys, hinting about the truth of Chihiro's identity.
During The Mole scene in Episode 5, Monokuma says he can tell them anything "aside from my three sizes", giving away that the mastermind is a woman.
Stage play:
In this version, Leon outright shows Sayaka how to spell his name.
