• Expy: Elly has an uncanny resemblance to Elle from Terranigma, both in name and appearance
    • Rico is a dead ringer for Blanka. No one is quite sure why.
    • Emeralda is a green-haired orphan sort of child that grows up within the game. Just like Rydia.
    • "I am Darth Vader Master Asia Graf Grahf, the seeker of power. Doth thou desire the power?"
  • Hey, It's That Voice!: So very many in the Japanese version.
  • Memetic Mutation: "Remember, kids...Chu-Chu died for your sins!"
    • "Did you just see my MAD SKILLZ?"
  • Shout-Out:
    • Super Dimension Gear Yggdrasil IV. Also, Giant Robo's basic design and piloting method are used by Seibzehn.
    • Seibzehn and Achtzehn, being the fusion of man and machine, are also a nod to Number 17 and Number 18. It's also a Bilingual Bonus.
    • The ancestors of Bartholomew Fatima and Sigurd Harcourt are Roni Fatima and Rene Fatima. This is a Shout Out to royal Final Fantasy VI brothers Edgar Roni Figaro and Sabin Rene Figaro. As another Shout Out to FFVI, Sigurd's surname Harcourt is shared by Duncan Harcourt, who was Sabin's martial arts mentor.
    • One of Billy's special attacks is clearly a Shout-Out to Doom
    • A "Ticketmiester" vendor in Solaris.
    • Amuro called. He wants Magnetic Coating back.
      • Domon would also like to have a word regarding Weltall Mk. II and its System Id, as would Ramba Ral regarding Brigandier/Andvari's weapons. And Aerods? More like funnels. They're even housed in the skirt armor when not in use.
    • At one point we have main hero and his rival use theit Gears to push away a massive falling object. Seems slightly familiar, no?
    • The creature in the sewer is named Redrum.
    • There's a poster of Tifa on the wall in one of the second class district residences in Etrenank. And while we're on the topic, Solaris' foodstuffs are processed by a facility referred to as the Soylent System. No prizes for guessing what the secret ingredient is...
    • Andvari's origins and introduction: see Panzer World Galient.
    • Name any super robot show that features no less than three robots performing a GATTAI sequence and you'll find your reference in the G-Elements.
    • Kahran Ramsus has an obsessive grudge against the protagonist and challenges him to battle at every opportunity, only to have his clock cleaned every time.
    • OR-Weltall's posture is remarkably similar to the Master Gundam. Unsurprising, considering who pilots it. In battle, it also sports a few rather notable aesthetic similarities to Deathscythe Hell Custom.
    • The meager efforts of you land dwellers are insignificant to the true and only power.
    • That's bound to get us into trouble with the makers of Star Trech!
    • Shevat contains a few references to Zeal. A floating city where one can find a Sage's hidden room, strange talking creatures (Chu-chus to Chrono Trigger's Nus), and Queen Zephyr (though she doesn't gain immortality by her own choice, and she's not quite as batshit insane). And speaking of Chrono Trigger, be sure to say "hi" to Lucca before you head out from Lahan...
    • Fei gets frozen in carbonite. He gets better.
    • The Gazel Ministry's personality data is housed in a supercomputer called SOL-9000.
      • The Zohar is also a reference to the Monolith from 2001. Its technical name in Perfect Works (Magnetic Abnormal Matter - MAM) also mirrors the Monolith's technical name from the 2001 novels (Tycho Magnetic Anomaly - TMA).
    • Gaspar, Balthasar, and Melchior are in the game as shout-outs to both biblical Fanon and Chrono Trigger.
    • The planet orbiting floating city/space station Solaris is a shout out to the novel Solaris by Stanislav Lem.
  • Urban Legend of Zelda:
    • A few of them, the two most prominant are that you can somehow use Elly/Sophia's OmniGear El Regerus outside of the one scripted battle it appears in, and that you can recruit Ramsus as a playable character after Elly merges with Deus).
      • These two originate from translated production notes in the Perfect Works books, outlining plans for El Regerus, Ramsus, and even Margie to be fully playable characters, only to have them get cut down to NPC status thanks to time and funding shortfalls.
    • Hilariously, you really can get the El-Regrs (Elly's Omnigear) by entering the final floor of the last dungeon and then going back out, but since its pilot is no longer in your party, it is useless. It's also playable in the Kislev battling minigame, but who enjoys grinding that?
    • For extra fun, it's possible to hack El Regerus into the game before Elly takes off, but it doesn't have a model for the overworld, causing a game crash.
    • There seems to be a rumor of a planned Xenogears OVA that takes place during the Zeboim era. So far, there's no evidence that such a thing was even planned.
  • Word of Dante: The idea that Yui was Shevat's premier warrior and defeated Citan in a duel was actually a result of a fan mistranslation of Perfect Works. It has since been embedded into the community's image of her.
  • You Fail Biology Forever: The game writers seem to have some... interesting... ideas about how DNA works. Fan translations of Perfect Works have revealed that the weird backstory justifications for some of the technology in the game takes this Up to Eleven.