The resurrection spell Athelas and its lesser version Thelas, at least one of which is present in every Trails game, reference the athelas herb from The Lord of the Rings, which has healing properties.
The character Cassius Bright gets his name from Paolo Cassius and Bright Noa, the two men to captain the White Base, the mothership of the titular Mobile Suit Gundam.
In the English version, during the ending walkabout sequence in Grancel, one NPC is taking a picture of his daughter and says "Okay, say "fuzzy pickles"!"
From the empty chest messages added in the English-language localization:
One in Sky the 3rd is "Judge a dungeon not by the color of its textures, but by the content of its treasure chests.", parodying Martin Luther King, Jr.'s I Have a Dream speech.
In The 3rd, when Kevin indicates that he wants to change his Dominion title the name suggestions include Black Arrow (which could be a nod to either the famous arrow of Bard from The Hobbit or the Robert Louis Stevenson book) and Blue Comet (a color-shifted reference to Char Aznable the Red Comet).
Kurt's description of a book he's reading in the prologue of SC is suspiciously similar to The Art of War, and Nial outright quotes Sun Tzu in FC.
Weapon names:
One of Kloe's weapons in Sky FC is named Hauteclere.
One of Joshua's weapons in Sky SC is named Strider, one of Aragorn's names from The Lord of the Rings.
One of Schera's weapons in Sky SC is named Galient Sword.
Tio's Orbal Staff exhibits a few similarities to the Intelligent Devices from Nanoha, Raising Heart in appearance and Bardiche in function. Her crafts Ether Buster and Beam Zanber even invoke the names and complete animations of Raising Heart's Divine Buster and Bardiche's Jet Zanber (or just Bardiche's Zanber Form in general). The very first weapon upgrade you can buy for Tio is even called the Lyrical Cane, and its in-game item description ends with "Magical!", which references Nanoha's incantation "Lyrical Magical" that she used in the first season.
As another Nanoha reference, this time to StrikerS, Elie's craft Cross Mirage shares its name with Teana's Intelligent Device, which is a handgun just like Elie's weapon. The animation for Elie's Cross Mirage even resembles Teana's signature attack, Crossfire Shoot.
A secret quest involves catching a group of hooligans styling themselves as the "High Bloods" for reckless driving. When you finally catch them and the Crossbell police demand their names, two of them give them as "Seymour Butz" and "Hugh Jass," both of which are gag names used by Bart Simpson when making prank calls to Moe's Tavern.
From the empty chest messages added in the English-language localization:
In Zero, a silver chest in the Mainz Mountain Path - Tunnel says "You took everything from me… Everything! … Well, at least I still have my charming personality."
In Zero, a chest in Ancient Battleground reads "Uh... Ugh... (That item was for Chestlene's schoolin'...)" This is a reference to Barret Wallace's line in Final Fantasy VII when Cloud Strife demands 3,000 gil for the next mission - "Uh......ugh...... (That money's for Marlene's schoolin'......)"
In Zero, in Revache & Co, you can find a chest full of sepith quoting Scarface (1983).
In Crossbell...first you get the sepith, then you get the mira, then you get the women.
In Zero, a chest in Revache & Co reads "Annie isn't okay. She wants you to arrest the smooth criminal." This is a reference to a Michael Jackson song.
In Zero, a chest in Revache & Co reads "Just when I thought I was out...they loot me again."
One in Zero contains a parody of the lyrics to "Highway to Hell" by AC/DC.
I'm on the highway to BELL(guard) ♪ On the highway to BELL(guard) ♪ Highway to BELL(guard) ♪
One in Azure is "To be fair, you have to have a very high IQ to understand police-stealing-from-treasure-chest jokes. The humor is extremely subtle, and without a solid grasp of Crossbell State law, most of the jokes will go over a typical player's head.", referencing a meme from the Rick and Morty fandom.
In Azure, you can find a chest in Geofront D lamenting the political situation to the tune of "Stuck in the Middle With You" by Gerry Rafferty and Stealers Wheel.
Erebonia to the left of me, Calvard to the right. Here I am, stuck in the middle with loot.
One in Azure jokes about Tio creating a handheld game console called the Tio Geo Pocket.
One in Azure states that Zeit was going to be the Crossbell Police Department's new mascot, but they wanted him to wear a trenchcoat and say the catchphrase "Take a Zeit out of crime", a reference to McGruff the Crime Dog.
In Azure, in the Azure Tree, you can find a chest singing "Eight Days a Week" by The Beatles.
Hold me, Noey ♪ Hold me, Noey ♪ I ain't got nothing but love, babe ♪ Eight days a Seek ♪
In Azure, another in Stargazer's Tower is singing "Paradise City" by Guns N' Roses.
Take me down to the Crossbell City ♪ Where the Pleroma is blue and the girls are pretty ♪ Oh, won't you please take me down? ♪
The one for raising a character to level 50 in Zero is titled "Crossbell Five-O."
The ones for winning large numbers of battles in Zero come from the lyrics to the song "I'm Gonna Be (500 Miles)" by The Proclaimers. The one for winning 500 battles is titled "I Would Kill 500 Foes...", the one for winning 1000 is titled "...And I Would Kill 500 More...", and the one for winning 2000 is titled "...Just to Fall Down at Your Door." A chest message in West Crossbell Highway in Azure sings it, but replacing miles with selge.
Moulin Rouge is named after the movie Moulin Rouge!.
Oiseau Bleu is named after the French fairy tale L'oiseau bleu.
Crossbell City is built on top of a large underground network called the Geofront. So is Tokyo-3 in Neon Genesis Evangelion.
Arc en Ciel is a reference to Cirque du Soleil. Both groups do the same types of acrobatic performances with elaborate costumes, and both have French names that refer to objects in the sky. Soleil means "sun", while arc en ciel means "rainbow".
When Jona denies being responsible for the fire-spitting robots in the Geofront C Sector, Randy comments "Your nose is growin', Jon-ster," a reference to The Adventures of Pinocchio.
During her shared victory quote with Kurt, Sara tells him, “If my name’s lightning, I’d better be very, very frightening.”
When entering a hazardous floor in the True Reverie Corridor, Nadia may say "Danger zone!" with the same inflection as the Kenny Loggins song of the same name... or, perhaps, Sterling Archer's own appropriation of that phrase.
The MKE Maus enemy from Cold Steel IV returns; in addition to its name referencing Mickey Mouse, Reverie gives it a new description lampooning how overprotective Disney is of its IPnote The part about it living "in damp habitats" references the swampy location of Walt Disney World and was carried over from Cold Steel IV.:
"A territorial rodent monster found in damp habitats. It mercilessly takes down any who infringe on its property."
Achievement names:
The one for seeing every Daydream is titled "I Dream of You."
The one for filling the fishing section of the notebook is titled "Fish Fear Me," referencing a popular series of T-shirts and hats featuring the slogan "Women want me, fish fear me."
During Nadia's S-Craft, she says "Welcome to my Teddy Talk."
One set of enemies you can face in a Shuffle Scuffle are the Habanelien Black and Habanelien Black RX, referencing the naming scheme of Kamen Rider BLACK and Kamen Rider BLACK RX.
Lapis's Brave Order is called Palace Coppelion, which comes from the ballet Coppélia.
During the Daydream "Ultimate Wilderness Cooking," commenting on the sniping between Roselia and Marquis Ballad, Altina states "They're hot and they're cold... they're 'yes' and they're 'no'... It's quite illogical behavior," referencing the lyrics of the song "Hot N Cold" by Katy Perry.
During the finale, Randy jokingly refers to Lloyd as Captain Crossbell.
Olivier's ultimate and penultimate weapons are both references to Wolfgang Amadeus Mozart: his penultimate is Eine Kleine, and his ultimate is Amadeus's Inspiration.
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