- Every Psync chapter title is a play on Singin' in the Rain.
- Ota's light novel pen name is Odoin Kyoma, which he chose an an homage to a popular fictional character.
- A-Set's last name, Sagan, is a tribute to Carl Sagan.
- The game has several references to Uchikoshi and Spike Chunsoft's previous collaboration, the Zero Escape series.
- The memorable "ca-clunk" that accompanies the initial 360-rotation of each escape room in Nine Hours, Nine Persons, Nine Doors is used during the initial pan over each Mental Lock in a Somnium stage.
- A late-game Somnium contains doors with letters painted on them in a similar style to the numbered doors of Nine Hours, Nine Persons, Nine Doors.
- When Date finds Manakas frozen corpse, he temporarily refers to her as Alice, short for All-Ice.
- Examining one of the autographs in the Matsushita Diner when within Mayumi's Somnium has Aiba observe the name to read "Hongo" and that she can't picture his face. Gentaro Hongo, aka Ace, the Big Bad of 999, was face-blind.
- A hostess named Reika from a club called Tiefblau is referenced a few times, a term from Ever17: Out of Infinity - another game Uchikoshi worked on in the past.
- Multiple ones to Danganronpa:
- If you examine a broken Panda ride at the scene of the crime when you are accompanied by Iris, she will say that she hopes the black and white bear doesn't punish her.
- In Mayumi's Somnium, there is an autograph board from Junko Enoshima. Examining it will trigger the BGM of the series' iconic Monokuma Theater.
- Examining the dashboard with Iris in the car at one point will trigger this dialogue:
- Iris: Dangan...
- A running gag is that Date "can't remember" the name of the forensics investigator Kagami. One of the incorrect names Date uses is Kodaka, a reference to Danganronpa creator Kazutaka Kodaka.
- During Mizuki's route, she and Date face off in So's garden in the rain against a horde of identical-looking bodyguards in suits, all wearing sunglasses and earpieces.
- During Ota's Psync session, Aiba has the option to skate on a patch of ice to destroy it, with Date jokingly calling her Yuri Katsuki.
- Also during the Psync with Ota, Aiba can punch a metal plate. While she does so, she asks Date if he's upset, to which he replies that he's not upset, referencing a skit from Pop Team Epic.
- Iris's favorite game is called ShovelForge, a clear reference to Minecraft.
- After glitching out Iris's ShovelForge dream, Date asks if it's August 32nd, a reference to a famous glitch in the Japan-only game Boku no Natsuyasumi. The art style in this part of the dream also resembles some of the more colorful texture sets in LSD: Dream Emulator.
- Examining a dragon statue in the Kumakura Office will prompt Date to ask if it grants wishes. Aiba tells him it is not Shenron.
- Examining the topiary at one point will result in the plant being labeled as a giant green blob that disappears when four connect.
- Examining an oil drum with Iris in the cold storage will prompt her to say "Hi, I'm Drum-aemon!"
- While explaing the Mandela Effect, Iris quotes an "electric mouse from that video game" and its tail being commonly misremembered to have a black tip as an example.
- When Date asks Iris what she would do if she stops time, she says she would try to catch a sky fish. This is a reference to how you obtain the Sky Fish soul in Castlevania Chroniclesof Sorrow.
- Examining the island in So's garden at one point has Date mention that "little island" translates to "kojima" in Japanese.Aiba: Director Kojima is here?!
- When inspecting the windows in Sunfish Pocket, a british chef can be heard berating one of the cooks.
- In Ota's Somnium:
- Right after Ota evades a close shave from the murderer, he mutters, "If this was Another, I would've died already!"
- Ota's Tokusatsu belt and the theme that plays during his Somnium clearly references Kamen Rider V3. He even says quotes from several Kamen Rider series:
- One of Ota's poses has his arms shape in an 90 degree angle, just like Ultraman.
- In the beginning when Syncing for the first time, Aiba appears in a kneeling pose with electricity surrounding her.
- When Aiba and Date discuss who 'Alice' is, one of the dialogue choices is "Adrian?" Pick it and...Aiba: Adrian!Date: Rocky!
Shout Out / AI: The Somnium Files