My favorite references out of the billion that are in this game:
Generic references
Bass line of the battle theme and melody of the victory theme from the first six games
Using a gold chocobo to access some hidden island that isn't visible on the map
Garnet's coat in the beginning is a white mage's outfit
Vivis' outfit is that of a generic black mage
Random NPCs wearing red mage outfits
The theme of crystals being a source of power throughout the world/universe
The toymaker who made the Mini- Burmecia, Brahne, and Cid figurines is named Gogo (mime from FF5/FF6)
"No cloud, no squall shall hinder us!"
FF1
Mount Gulug/Gurgu Volcano music
Ice Cavern
Garnet's real name is Sarah and her mother is named Jane, like Queen Jayne and Princess Sarah
Princess Cornelia from the play likely being a reference to Corneria
The Beautiful Potion and Strange Potion descriptions both mention Matoya
The Four Fiends
The Rat Tail
FF2
Hilda is named after the resistance leader
The
Hilgigars (Hill Gigas) enemy
Pandemonium (and the music that plays there)
The story that Ramuh asks you to put together when you meet him is based on part of the storyline
"Once upon a time, 33 small countries fought together against an empire. One day, a rebel troop visited a man named Joseph, who lived with his daughter. Owing a debt to the troop, he gladly accepted their pleas for help. They headed for a cavern in the snow field. With Joseph's help, the troop defeated the Adamantoise in the snow field cavern and acquired the Goddess Bell they needed to enter the empire's castle. On their way home, they fell into a trap set by a traitor. Joseph gave his life to save the troop. The troop left without telling Joseph's daughter, Nelly, about the tragedy. Historian's explanation: Although Joseph's death was not reported to his daughter, the manner of his death speaks for itself. This is the story of a true hero."
FF3
The Invincible
Une's Mirror and Doga's Artifact (and their affect on the music player at the Black Mage Village)
Thematic parallelism between Kuja and Xande (and Necron and Cloud of Darkness)
Both fearing their mortality, Xande and Kuja unintentionally perform globally-perilous actions that lead both Necron and Cloud of Darkness to enter into the mortal realm and decide to revert the world to nothingness. Also, both Necron and Cloud of Darkness did not show up until the ending story as well as appearing as a final boss. The final boss music accompanying these encounters is also structurally similar.
Moogles obviously
FF4 (a lot of good ones)
Kain's Lance as a weapon
Zorn and Thorn using Palom and Porom's Twincast ability to let each other cast Flare and Comet/Meteorite
Namingway Card and its function
Cid's last name
The appearance of the first Hilda Garde ship looks a lot like the Lunar Whale
The Antlion that's supposedly tame but attacks a prince
There are two moons in FF4, referenced in the Ultimania as the
Gaia and
Terra moons; one is red, and one is blue
Zidane and Kuja's relationship is somewhat similar to that of Cecil and Golbez, being brothers from another world
Vivi uses Fire to melt an ice blockade, like Rydia
The destruction of the summoner tribe
The old man who gives the player the Excalibur in exchange for the Magical Fingertip is Kokuro (the dwarven blacksmith from FF4)
"Rally-Ho!"
FF5
Boco card and Bobby Corwen
The icon on the Airship card (or maybe that's also from FF4?)
The moogle theme playing at Mognet Central
Gilgamesh
Kuja's Theme and the melody from
this song
The Lancer Ability
Using the item Soft to instantly kill enemies made of stone
Tantarian's resemblance to the book monsters (the
cover has images of
Page 128 and
Page 256, while
Tantarian itself looks like
Page 64)
Grand Cross spell
Necron's resemblance to the Necrophobe enemy
Nova Dragon as Shinryu
Atomos obviously
The Stellazio lady is named Stella, which was the name of Bartz's mother
And didn't summoners have hats with horns on them in FF5?
FF6
Trance ability
A man in Lindblum named Locke
Madeen/Maduin
Mog
The Ahriman enemy is named Veteran again
Flare Star
The three statues in the Desert Palace
The menu screen calls the area around the Chocobo Forest the
King Ed Plains
Alexandria has a astatue commemorating General Madelene (Madelina was Terra's mother)
Eidolons are acquired through gemstones the same way espers are learned from magicite
Also I think FF6 was the first appearance of Ultima Weapon
FF7
The band playing Rufus's Welcoming March ("Hey, not bad!")
Buster Sword in the Lindblum weapon shop
Little girl in Lindblum named Elena
Climhazzard
Using chocobo footprints
Kupo Nuts
Similar foundational life cycle (when someone dies, their soul/Mako returns to the planet's Crystal/Lifestream)
FF8
Amarant's No Mercy ability is Seifer's Limit Break (and they look similar)
Quina's Eat command
FFT
Reis's Wind and Cherry Blossom
A bunch of Steiner's attacks
A ridiclous number of item names (Robe of Lords, Germinas Boots, Maximillian, Save the Queen, etc.)
Auto-Potion support ability
Chocobo's Mysterious Dungeon
One of the Mognet moogles is named Atla
Parasite Eve
In the Lindblum Synth Shop, the owner is named Torres, and the man at the counter is named Wayne. These were the two people in the NYPD weapons room. In addition, when you first enter the said shop, the two of them have a skirmish which is practically the same as the "safety vs. power" lecture you overhear when you first enter the NYPD weapons room.
Vagrant Story
The Alexandria barkeep is named Ashley, and has a very familiar hairdo
Other stuff
"Dammit Jim, I'm a doctor, not a miracle worker!" - man near the air cab station in Lindblum; Star Trek
"Resistance is futile" - Black Waltz #2; also Star Trek
"Fear leads to anger. Anger leads to hate. Hate leads to suffering." - Necron; Star Wars
Marcus and Blank referred to as "those good ol' boys" by Ruby; Dukes of Hazzard
"I'm Kupo for Kupo Nuts!" - one of the moogles; Cocoa Puffs
"Great Scott!" - man being chased during the Festival of the Hunt; Back to the Future
Shakespearean references - Prince Puck,
I Want To Be Your Canary, the character of King Leo (King Lear), and the author "Lord Avon" (as Shakespeare was called the Bard of Avon)
Jabberwock and Bandersnatch - Lewis Carroll's
Jabberwocky
The relationship between part-Time Worker Mary and Jobless Jeff (owners of the Vega and Altair shops, respectively) mirrors the
Tanabata legend
The Cleyra dance ceremony is obviously traditional Irish dance, thus Fratley is probably named after Michal Flatley
Madain Sari is named after a pre-Islamic archaeological site in Saudi Arabia called Mada'in Saleh; in the Qur'an, the people of Mada'in Saleh were a tribe that fell to the worshipping of idols.
The statue of General Madelene that I mentioned earlier may refer to Joan of Arc
Tantalus is named after a large volcanic crater in Honolulu, near the area where a great deal of FF9 was developed
They've all been pointed out countless times before, but these are my favorites of the bunch. It's the little things in life.