Many of the attacks Monokuma uses on Monomi throughout the game are references to many famous attacks/characters from classic Shonen Jump manga.

• In Chapter 2, Monokuma uses the "Pegasus Meteor Fist" technique from Saint Seiya.
• In Chapter 3, Monokuma's punch references Rohan Kishibe's stand, "Heaven's Door" from JoJo's Bizarre Adventure.
• In Chapter 4, Monokuma uses the "Nine Headed Dragon Flash" technique from Rurouni Kenshin.
• In Chapter 5, Monokuma uses rapid punches and shouts "ORA ORA ORA" referencing JoJo's Bizarre Adventure.

The game uses mist overlays during the "Man's Nut" shower scene to cover up Mahiru and Hiyoko, but the base image is more revealing, including drawn nipples for Mahiru.

In one scene in Chapter 1: Destination Despair, Miharu takes two photos of all the students during a party. In one of these photos, Hajime can be seen holding a wine glass filled with an orange liquid, presumed by fans to be orange juice. His appearance with the drink in this image evolved into a recurring meme among English fans of the game, though its origins are unclear, with the earliest known mention on social media possibly being a 2013 Tumblr post. The meme was later acknowledged in a tweet by series creator Kazutaka Kodaka in 2024.

In Japan, Danganronpa 2: Goodbye Despair and Danganronpa V3: Killing Harmony are known as "Super Danganronpa 2: Goodbye Despair Academy" and "New Danganronpa V3: Everyone's New Semester of Killing" respectively. According to Danganronpa 2 director Takayuki Sugawara, the "Super" prefix was chosen by the second game's staff to indicate that they wanted to improve and surpass the first game, having been inspired by Famicom and Super Famicom games they grew up playing. According to series creator Kazutaka Kodaka, the "New" prefix was added to Danganronpa V3's title to continue this trend in anticipation of the game's reveal at a Sony press conference in September 2015.

During the 16-bit era of video games, it was a regular practice for developers to include the adjective "Super" in the titles of sequels to older games for the same reasons it was added to Danganronpa 2, which expanded on the lore of the first game while changing other gameplay elements. In the modern era of video games, this trend evolved into adding the word "New" (新, "shin") instead to indicate that it is a new spin on an older game, which Danganronpa V3 did to show it was meant to be a new take on the series formula while being almost disconnected from the lore of previous games.

During a Q&A with Kotaku in 2015, it was noted that both Danganronpa: Trigger Happy Havoc and Danganronpa 2: Goodbye Despair had a female character that appeared to have been designed to be the player/main character's favorite, the former game having Kyoko Kirigiri and the latter game having Chiaki Nanami. When asked if this was intentional, series creator Kazutaka Kodaka stated: