- Most prominently, several characters are named after characters from Dante's The Divine Comedy, with Beatrice being the most obvious. There's also Virgilia (Virgil, Dante's first guide through Hell), and Clair vauxof Bernard (Bernard of Clairvaux, who is Dante's final guide through Heaven).
- Many of the fantasy characters are named after demons listed in Ars Goetia.
- The entire scenario on Rokkenjima is a reference to And Then There Were None, and the work itself is referred to by name several times.
- The entire plot, from a mystery perspective, also pays homage to another Agatha Christie classic, "Hercule Poirot's Christmas". To wit: an unpleasant and domineering family patriarch organizes a family reunion for motives of his own, only for murder to be committed by his well-concealed illegitimate child.
- And the revelation of EP 8's Tooya Hachijo is a reference to the ending twist of The Fourth Door by Paul Halter.
- There are several references to Touhou:
- In the original sound novels and the anime, Jessica cosplays as Marisa Kirisame for her band's performance. In her and Kanon's ending in Ougon Musoukyoku, she dresses up as Marisa again and has Kanon cosplay as Reimu.
- In EP7, Gaap jokingly calls herself "U.N Owen, a 495-year-old witch", referring to Flandre Scarlet, who's a 495-year-old vampire, and her famous Leitmotif "U.N Owen Was Her?".
- Maria's favorite show is Card Master Sakura, and she originally wanted to name Sakutarou after the heroine of the show but later changed it to sound more masculine.
- In Episode 1, Rudolf pulls on Battler's ear in the sequence of the Konami Code.
- According to Ryukishi07, Battler's habit of pointing dramatically was inspired by Phoenix Wright.
- One of the background tracks, system0, opens with lines sampled from Star Trek: First Contact.
- Sayo Yasuda's nickname "Yasu" is a reference to Yasuhiro "Yasu" Mano, the player character's detective partner in The Portopia Serial Murder Case.
- Beatrice's name could have been possibly inspired by Jessica Fletcher: The latter's middle name is Beatrice and is also involved heavily in murder mysteries.
- In EP4, Gaap says she got her outfit from "Devilish Pretty", which references the popular real-life Lolita clothing brand Angelic Pretty (and her outfit is also inspired by an actual dress◊ made by that brand).
- Kyrie, Asumu and Ange were named after Priest skills from Ragnarok Online.
- At one point, Beatrice mentions that she owns a Moon Stick.
- During Krauss' battle with the Goat in EP4, it mentions that his punch would have the power to easily win the first Tenkaichi Budokai, referencing both the game and the infamous Over 9000 meme.
Shout Out / Umineko: When They Cry