- The most pervasive and obvious is to Dungeons & Dragons, as the story takes place in "the future" of a D&D-esque medieval fantasy setting, with many of its tropes used, subverted, or played with in the contemporary, multi-racial setting. Nonhuman races are somewhat-recognizable versions of various D&D creatures, with standard D&D premises about them often treated as humans' stereotypes of those races. Vancian Magic is not used, but magical weapons and such are quite similar to D&D magical items...except when they aren't what they sound like. For example, Rings of Protection are contraceptive items. In a more direct fashion, MU's health facility is named the Gygax Memorial Healing Center.
- The Lord of the Rings gets a couple of prominent nods:
- The university employs a lawyer by the name of Mitch McSmeagol.
- Shiel makes mention of a creature from the surface that supposedly lived in a subterranean lake near her home. Her description of it is a dead ringer for Gollum.
- Gnomes are essentially hobbits in all but name. They live in shires and don't wear shoes. "Halfling" is considered a racial slur. Some of them have a certain propensity for adventures, though they consider the very concept quite improper and really don't like to talk about it, to the point that Hazel gets put off her dinner by the group discussing adventures in Y2-137. However, they have a cultural tradition of "forming a fellowship against the darkness" when hard times come around. Hobbits' natural stealth, in gnomes' case, translates as a combined Perception Filter and Weirdness Censor that gets stronger the more of them are in one place.
- Hazel learned lockpicking because "you never know when Old Grayrobes will come knocking." It's a Gnomish saying, in fact.
- Steff dismisses the idea of elves and dwarves hanging out as "just like a fellowship in a storybook."
- The Leeroy Jenkins meme is played on by Mack's lawyer, Lee Jenkins, who fits the name but inverts the typical personality.
- One chapter contains a description of a young boy playing out a fantasy battle scenario with toys, including a part where "the boy added a hellhound with an anti-magic shell and immediately one-upped himself with a behemoth that quite improbably fed on anti-magic hellhounds." (The fantasy version of an attack dog with built-in forcefield and a dinosaur who eats forcefield dogs!)
- The second-year OT story "Magisterius University and the Methods of Obstinancy" is one long homage to Harry Potter and the Methods of Rationality.
- The in-universe equivalent of Occam's Razor is "Durkon's Hammer".
- One history class was entirely devoted to making a "the cake is a lie" gag.
- More Tales of MU had "I call it Vera" directly quoted.
- The "Stone Soldiers" game which forms a foundation for some of the interactions with Hazel and the second-year storyline revolving around Acantha is a homage to miniatures-based tabletop wargames such as Warhammer.
- The OT story "The Centre Cannot Hold" contains a prominent theme from Warhammer 40,000, with the "evil star" Malbus as a Negative Space Wedgie through which monstrous chaos beasts occasionally force their way into the MU-niverse to wreak havoc following the same lines as daemons and Chaos Space Marines entering the Materium through Warp rifts like the Eye of Terror or the Maelstrom in 40K.
- According to Lore professor Fenwick Hall, "The people of Whale Island tell of the sorcerer-king who came out of the sky in a basket of whicker and traded a handful of emeralds for seal-skins to repair his… this is the exact translation… ‘gas-bladder'."
Shout Out / Tales of MU
Tales of MU features a lot of references to other media.