The cry of the dwarves, "Rally-ho!", is a mistranslation of Lali-ho, the cry of the dwarves in Final Fantasy IV.
If you examine a sword that looks remarkably similar to the Buster Sword in the weapon shop in Lindblum, Zidane will remark "I remember a guy with spiky hair who carried something like this...", referencing Cloud from Final Fantasy VII.
One of Zidane's lines towards the end of the game is "No cloud, nor squall shall hinder us!"
A sidequest reveals that Princess Garnet's real name is Sarah, the same as the princess from the original Final Fantasy I.
If you examine the grandfather clock in Quan's Dwelling, you are told that there is nothing inside. This is in reference to Final Fantasy VI, where there would be an Elixir in every grandfather clock in the game. This is the only place in Final Fantasy IX where there is a grandfather clock you can examine, so it was likely an intentional reference.
When Princess Garnet is first encountered, she wears a robe like that worn by the White Mage in the original Final Fantasy I.
The world map bears a striking resemblance to the world map in Final Fantasy I.
The Show Within a Show play "I Want to Be Your Canary" features a character named Princess Cornelia, a reference to Coneria (renamed "Cornelia" in later translations) from the original game. Since her father is named King Leo, this is also a reference to King Lear (see the entry on Shakespeare, below).
The four elemental fiends fought in Memoria originally appeared in the first Final Fantasy, though Marilith's name is mistranslated as "Maliris" in Final Fantasy IX (this fiend was called "Kary" in the NES version of Final Fantasy, though later translations used the name "Marilith").
Freya's can find a weapon named Kain's Lance, referencing Kain Highwind from Final Fantasy IV.
In one scene in the Black Mage village, a couple of Black Mages are talking about naming a chocobo "Bobby Corwen". The first syllables of those two words, "Boco", refer to Boko, Bartz's chocobo from Final Fantasy V.
The final boss, Necron, uses an attack called Grand Cross, the same name as an attack Exdeath uses in Final Fantasy V.
The Limit Break in this game is called "Trance", which first appeared in Final Fantasy VI as one of Terra's skills after she unlocks her Esper power. It was translated as "Morph" in the original SNES version of Final Fantasy VI.
Zidane's ultimate weapon is called Ultima Weapon, which is a recurring weapon in the series (it's also known as the Atma Weapon in the SNES translation of Final Fantasy VI).
Three of the attacks that Carbuncle can use, Ruby Light, Emerald Light and Diamond Light, refer to Ruby WEAPON, Emerald WEAPON and Diamond WEAPON from Final Fantasy VII.
Could be a coincidence, but one of the "SFX" moves during the stage fights at the beginning of the game (flashy moves that do no damage) is called "Meteo", which could refer to how the spell "Meteor" was shortened to "METEO" in the SNES and PS1 versions of Final Fantasy IV.
Necron quotes Yoda before the fight with it. ("Fear leads to anger. Anger leads to hate. Hate leads to suffering.")
After fighting Steiner for the first time, he collapses, remarking "Bah! Only a flesh wound!", a reference to the Black Knight scene from Monty Python and the Holy Grail.
There are a few references to William Shakespeare, namely that the prince of Burmecia is named Puck (the name of a character in A Midsummer Night's Dream) and the author of "I Want to Be Your Canary" is Lord Avon, a reference to Shakespeare himself who was often called the Bard of Avon.
Zidane having a monkey-like tail is a possible reference to Dragon Ball. There are strong similarities in backstory between Zidane and Goku.
Sir Fratley could be a reference to Michael Flatley, the Irish dancer renowned for the Riverdance.
Which is also referenced to the dancing Freya and the others do in one scene, which looks very Riverdance-esque.
Two workers in the Lindblum Synthesis Shop argue over whether or not it is better to have a strong weapon for power or a strong armor for safety. This is a reference to two officers from Parasite Eve (also made by Square) where they had a similar argument; one wanted stronger guns while the other wanted safer guns. Their names, Wayne and Torres, were reused for the characters in the synth shop.
Remember Part Time Worker Mary and Jeff from your first visit to South Gate? Although the entire exchange is largely seen as a Big Lipped Alligator Moment, it is actually a reference to this Chinese fairy tale.
In the Steam remake, you can net an achievement called Kain's Legacy when you obtain Kain's Lance, a nod to the Square-published game Legacy of Kain
Some of the names of locations are references. The town of Dali is named after Salvador Dalí. The library of Daguerreo derives it's name from the Daguerreotype, a very early form of photograph.
"Gaia" and "Terra" are the Greek and Latin words for "Earth" respectively.
Each of the party members behaves like a specific job class from a previous Final Fantasy game. Zidane is a Thief with some Ninja-like abilities, Vivi is a Black Mage (obviously), Steiner is a Knight (with Magic Knight abilities if paired with Vivi), Garnet is mainly a Summoner with some elements of White Mage, Quina is a Blue Mage (possibly part Beastmaster, depending on how you view the similarity between hir 'Eat' ability and the 'Capture' ability of a Beastmaster), Amarant is a combination of a Monk and a Ninja, Freya is a Dragoon (dressed as a Red Mage!) and Eiko is mainly White Mage with some elements of Summoner.
There's also Beatrix, who is clearly a Paladin, albeit with much stronger White Magic than most of them tend to have.
Although not the most popular of the series, Hironobu Sakaguchi himself has gone on record to say that this iteration is arguably his favorite and represents everything he personally holds to be at heart of Final Fantasy.
The official German PlayStation Magazine reported that the game was a continuation with a new character named Skylar Goodsworth. Turns out they were tricked by a fanfiction on what was then a rather obscure site, which not only lacked any form of professionalism, but came from a website hosted by Beepworld.
An early preview of Final Fantasy IX stated that it was to be a remake of the first game in the series. A writer clearly unfamiliar with Roman numerals claimed that Square had started development on "Final Fantasy 1 X".
Genre-Killer: The decline of video game strategy guides is sometimes attributed to the official American guide for this game. Square Enix, wanting to promote their site, Playonline.com, forced Prima to gut the entire thing and redirect users to the site for more info. Considering the game came out in 2000, it was outright impossible for many to connect to the internet and those who could found the site wasn't much better. Many purchasers ended up finding sites like GameFAQs, and many buyers thought it was the general direction of strategy guides from that point forward. Nowadays, Strategy Guides are usually only found in stores dedicated to gaming, and even then, it's usually only in a small section of it.
Offer Void In Nebraska: The Android version is only available to devices that has official access to the Google Play Store. Have a Kindle, Nook, Replicant device, Cyanogenmod device, an Android-compatible Blackberry phone or any other android devices that can't access the Google Store? You can't have it.
That you can get an alternate ending by beating the entire game in twelve hours. It is true that you can get the Excalibur II by reaching the final dungeon in twelve hours, but this one stretched credibility. Supposedly, the alternate ending involved a twenty-five year old Eiko killing Garnet and trapping Zidane in a crystal.
That if you name Garnet "Pleb", Steiner will give Vivi the Octagon Rod, a late-game weapon, much earlier than usual. There's no way to get the Octagon Rod until Disc 3.
The concept art for the "Rat Knight" ended up becoming Fratley and Freya, with genders changed and motivations split down the middle.
It's also kind of hard to not think of Amarant when looking at the Elementalist guy.
The entire game was originally planned as the first in a spinoff series made to appeal to old school fans. The game initially wasn't going to be released as 'Final Fantasy IX' - as developers feared the fact that it was so radically different from the previous two games would alienate gamers. Rumours circulated that it would be a side story outside the main series, before it was confirmed as Final Fantasy IX.
Concept Art shows Queen Brahne having a couch-sized cat and Garland would have beared more of a resemblance towards the Garland from Final Fantasy I.
Also, Thorn and Zorn were originally going to be just one character, an old man who was the court wizard.
Concept art shows that Hades was originally going to be the final boss in the game. Late in development Necron became the final boss, while Hades became an optional boss in the Memoria.
There were apparently at one point three additional Moogles involved the Mognet sidequest: Mogpi, Mogrody, and Mogribs. Their names appear in the game files, but they do not appear anywhere in the actual game.