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In general:

In General

While it was a major plot twist in the first game, essentially everyone knows nowadays that Junko Enoshima is the Big Bad of most installments in the franchise. Hell, it's impossible to look at any Danganronpa content online without seeing her in all of her villainous glory, including official promotional material. In fact, don't even bother searching her name in the "images" tab on Google or another search engine, since the VERY first image results will always show her together with Monokuma. The sequels don't help much as they make zero attempt in hiding this.

Danganronpa: Trigger Happy Havoc

Kyoko's talent being the Ultimate Detective is something people are well aware of, even before it's revealed. Just like Junko above, the following installments don't even bother hiding this.

Danganronpa Zero

The reveal that Ryouko is Junko with amnesia is easily the most well-known twist from the book. Even people who know nothing about the other points in the latter half of the story tend to know this.

Danganronpa 2: Goodbye Despair

Nagito having... very questionable morals and an obsession with hope. This is revealed fairly early on, but is a major twist that has relevant ramifications on the plot and heavily changes both the player and Hajime's view on him as a person.

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

Knowledge of Aoi's apparent death in the second episode of Side:Future spread very quickly.
Gekkougahara being the robotic avatar of Monaka spread pretty fast around the fandom.
Episode 9 made the tag #dr3 trend on tumblr, therefore, the deaths that happened in that episode, particularly Kyoko's and to a lesser degree Juzo and Ruruka's, became public knowledge.
Due to being heavily involved in the latter half of the plot and being half the reason why Side:Despair is so hated by many fans, Mitarai's brainwashing program has become widely known among the fandom.
Yukizome and Mitarai's Face-Heel Turns are widely known and discussed by fans, despite being major lategame twists (the latter doesn't even happen until the penultimate episode).
Due to the reasons about why Tengan manages to be heavily disliked by fans, him being the Mastermind became known by them.
Kyoko's survival in Side:Hope spread very quickly. The resurrection of the comatose students also became well-known in the fandom.

Danganronpa V3: Killing Harmony

Taken up to eleven, even by the standards of the franchise's fans. Thanks to some dataminers, a bunch of plot twists and deaths were spoiled before the game was even released, most infamously Kaede's revelation as a Decoy Protagonist and her execution.
The ending has quickly become very infamous among fans for its bizarre, sudden meta approach to the franchise. It doesn't help that a vast majority of the criticisms leveled at the game stem solely from it.
Korekiyo having a Brother–Sister Incest relationship with his sister has became a hard fact to avoid, due to the infamy of his motive combined with the already-odd manner in which be brings her up until then. The sheer memetic quality of this trait, and especially the "seesaw effect" have also made it difficult to avoid any kinds of jokes involving him and either incest or seesaws prior to Chapter 3, which can spoil his role in Chapter 3 as soon as the latter term comes into play.

Danganronpa Togami

The reveal that Blue Ink is Byakuya's sister Shinobu is easily one of the most well-known points about the novel, despite only being revealed near the end of the first volume.
Due to the controversy surrounding it, Shinobu's rape and the fact that Kazuya isn't Byakuya have become rather well-known.

Killer Killer

The series' status as a Stealth Sequel and Mukuro's role as Hijirihara's inspiration.