- Shirou's nightmare in episode 8, where swords erupt out of his body, is uncannily similar to how the Apocalypse Virus manifests in Guilty Crown. Actually a recursive Shout-Out, as the transformation and other things in Guilty Crown are a Shout Out to Heaven's Feel, which is what this foreshadows.
- Gae Bolg smashing its way through Rho Aias's layers of shielding strongly resembles the way a certain other franchise's Deflector Shields shatter like glass when they are overwhelmed.
- Shinji getting Illya's heart jammed into him by Gilgamesh and then promptly beginning to swell up like a horrific tumor strongly brings to mind Tetsuo's fate from the AKIRA movie. Viewers of more recent anime have also likened it to getting shot with a Dominator's Eliminator mode. Made funnier by the fact that Tomokazu Seki also voices in that series.
- Rin calls the Grail a "Monkey's Paw" in Episode 22.
- Also later in that episode, we find out that Rin's first memory of beginning to admire Shirou came when she saw him practicing a high jump over and over again after school. This may be a reference to how Mizuki becomes infatuated with Sano in Hana-Kimi, which was one of the biggest shoujo manga being published at the time Fate/Stay Night was originally released in 2004.
- This one may be more of a stretch, but there were some who noted that the core of the Holy Grail rising out of the mass of flesh actually somewhat resembles the Colossal Titan. Or it could be a reference to Giant Naked Rei.
- Episode 24 has lots more references to Neon Genesis Evangelion, including a cross-shaped giant explosion and a horrific bloody substance spilling out of a massive Humanoid Abomination and threatening to destroy the world a la LCL.
Shout Out / Fate/stay night [Unlimited Blade Works]