- The "Einzbern Consultation Room" specials from the DVD are basically a huge Shout-Out to the Tiger Dojo corners from Fate/stay night, complete with role reversal with Irisviel as the "teacher" and a teenage amnesiac Taiga as the "student". The segments contain a few other Shout Outs:
- "There are DDD circumstances behind that, so I'm sorry."
- Alba's silhouette can be seen when Iri talks about mages in the Nasuverse. His brief appearance at Alimango Island as a mage sent to torch the area mentioned above also counts.
- Some of the explanations about the world and Holy Grail War are set to South Park-style illustrations.
- Caster's vision of Jeanne D'Arc is the exact same design from Fate/Apocrypha.
- Caster is rife with references to the Cthulhu Mythos:
- His Noble Phantasm, Prelati's Spellbook: Text of the Sunken Spiraled City, is made from human skin, has a screaming face on the cover, and is also known as the R'lyeh Text. The lore behind it reveals it's either a translation of the Necronomicon or is a portal to R'lyeh itself sealed into a blank Bible.
- His invocation to summon an Eldritch Abomination in episode 2 is "Cthulhu fhtagn".
- The incantation he uses to summon the Cthulhu expy is "Ph'nglui mglw'nafh wgah'nagl fhtagn!"
- He's referred to as a Deep One in the "Einzbern Consultation Room" specials.
- Natalia smokes the same extremely rare brand of cigarettes that Touko does.
- Fate/Zero Materials notes that, after the war, Kayneth's Volumen Hydragyrum was tweaked a bit by Waver so it could assume the role of a household servant. The only problem is, thanks to being exposed to a certain film, it occasionally goes berserk while insisting it's a killer robot from the future.
- In Episode 14, the two F-15J pilots flying in to investigate Caster's monster trade some banter on how if they were in a kaiju movie, they'd be dead. One of them remarks that they would just be there to die before the "Giant of Light" shows up to kill it.
- Some of the weapons◊ in Gate of Babylon are identical to ornamental pieces sold by Kit Rae and United Cutlery. This fits somewhat, since they're all supposed to be Impossibly Cool Weapons.
- In the original website for the light novels, Jin Haganeya's introductory words (obtained by clicking on "Special" and "Jin Haganeya") for the series were taken almost word-for-word from Pixy's opening words in Ace Combat Zero: The Belkan War:Oh, her?Yeah, I know her.It's going to take a while.It happened years ago.Did you know... there are three kinds of kings?Alexandros III Megas.King Arthur.And Gilgamesh.Those are the three.And her...
Shout Out / Fate/Zero