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 otherfranchise'sDeflector 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.
In Episode 22, 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.
Rin and Shinji trapped in the mass of the Holy Grail nearly being crushed to death evokes Kaori's fate from, once again, AKIRA.
Different from the Evangelion references, Gilgamesh's last actions before being pulled into the Reality Marble are to laugh at Shirou, in a manner reminiscent of Iori Yagami.
