Y is for You're Trying Too Hard

... but I still like the Xenosaga series anyway for cramming itself as full of allusions (especially religious ones) as it can.

First, religious and philosophical allusions in Japanese RPGs and anime is nothing new. Neon Genesis Evangelion took it to a ridiculous level, starting with its title.

Here's a small, non-inclusive catalogue.

The titles of the three games: Der Wille zur Macht, Jenseits von Gut und Böse, and Also sprach Zarathustra. All of the titles from books by Nietzsche.

Earth: Lost Jerusalem (it's lost)

Orthodox Christianity resemblance in dress/setting: Ormus (including a Patriarch!)

Characters: Albedo, Rubedo, and Nigredo. All three are Jungian terms for human individuation.

Characters: (color) Testament.

Character: The android KOS-MOS. Kosmos. Universe, order, and harmony.

Character: chaos. Besides the obvious, is also called Yeshua.

Character: Abel. Yeah, that one.

Character: Nephilim. One of the more appropriate namings - she is rather ethereal.

Character: Ziggurat 8, nicknamed Ziggy. Nice way to tie in Mesopotamian architecture.

Character: Canaan, a Realian government agent.

E.S. Units: Reuben, Simeon, Levi, Judah, Dan, Naphtali, Gad, Asher, Issachar, Zebulun, Joseph, Benjamin and Dinah. Joseph's sons.

Ships: Woglinde, Dammerung. From Wagner operas.

Key Item: The Zohar, a monolithic artifact from Earth. Also has inscribed on it "bereshith." Hint: the start of the book of Genesis.

Key Item: Proto Omega... "Omega" being a symbol because that's really cool. Other things with Omega include Ω Universitas, Ω ID, Ω Res Novae, Ω Metempsychosis,
and Ω Metempsychosis.

Key Item: Vessels of Anima.

Group: Salvator faction - after the saint?

Place: Proto Merkabah, a giant ship they have to destroy.

Place: Labyrinthos.

Species: Gnosis. Sort of like spirits, I guess.

Gnosis: Abel's Ark - basically a really really huge intergalactic interdimensional creature.

Computer: Zarathustra. It's also a major boss in one of the games.

And that's only the start. The games are really great, especially the third one, but the only game that I've seen have even more ridiculous allusions is Xenogears: the game that would later come to spawn this trilogy.