"The Hedgehog Can Never Be Buggered at All" is among Nanny Ogg's favorite songs, while simultaneously a reference to Neon Genesis Evangelion's own discussion of the Hedgehog's Dilemma. The TV Show where the statement is made is an Expy of Look Around You.
The narrator notes that while regular firepower doesn't do much damage against the Angels, a viable option in the event of failure would be to Use more gun."
A lot of Command & Conquer characters work for NEG, with Anton Slavik, Oxnana Kristos and CABAL (as COEUS TITAN) being the most obvious.
Dr. Sylveste gives young Asuka a Geth as a robotic pet.
One Doctor Tam has been assigned to Project Evangelion after a "nasty family related incident". No good can come of this if River happens to get involved.
Rury may be a reference to Ruri Hoshino, both sharing her name (in a suitably Nazzadi-altered form), being a product of genetic manipulation and displaying a tendency to thank their A Is ("Thank you, Omoikane", "Thank you, COEUS", anyone?).
For some reason, this troper thought of the first fight with Tyler after reading about Shinji punching Toja.