"I'm of an older generation who grew up with classic giant robot anime by Nippon Sunrise (e.g. Raideen, Gundam, and Votoms). Besides the guy who enthusiastically created gear/AMWS/AGWS/ES mecha is more Takahashi than me. (His room is filled with vintage Chogokin Toys.) ;) "
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.
Soraya Saga created the characters of Edgar and Sabin, including way too much backstory to actually fit it all into the game and making not-quite-official tales of their childhood as a doujinshi. She was also one of the lead writers for Xenogears, giving her a chance to throw in lots of references to a pair of her favorite characters.
One of Billy's special attacks is clearly a Shout-Out to Doom
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.
Allenby's Gundam and her going berserk and having Domon give her a similar speech before defeating her are very reminiscent of Fei talking to and defeating a drugged up Elly in Vierge.
The Dark Gundam's penultimate form mutates organic wings, as (the location) Deus does. When traveling through its interior, Domon even goes through similar tunnels as the Xenogears party does. And, of course, there's the fact the love interest is assimilated with the Big Bad and is rescued by the protagonist. The last few episodes are where Xenogears's homages really begin to shine through, and this was all done intentionally, and as such it does nothing to make the endgame less awesome. See Sincerest Form of Flattery.
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.
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 batshitinsane). And speaking of Chrono Trigger, be sure to say "hi" to Lucca before you head out from Lahan...
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).