Freya's outfit is actually a Red Mage uniform, Vivi is also obviously modeled after the 8-bit sprite and Garnet wears a White Mage Robe when she first encounters Zidane.

Kuja's signature move Flare Star is the Ultima Weapons signature attack from FFVI

Garland's palace Pandemonium is a reference to the Castle of Hell that the Emperor uses as the last dungeon in FFII

The Magical Fingers Key Item references they belong to an artisan named Gogo

The FFV sprite of a Chocobo and airship are pictured on their Tetra Master card, their is a Namingway card as well that an NPC can use to rename a character just like Namingway did in FFIV.

Gaia has a red and blue moon which a reference to FFIV's two moons.

Garland is an alien guardian created to safe passage the souls of Terra and find them a new home. This is very similar to what FuSoYa and KluYa were tasked with doing for the Lunarians in FFIV.

The idea of life forms from one world merging and being reborn in the new world they land upon could be a reference to FF: The Spirits Within

Cid's last name Fabool is a reference to Yang's kingdom from FFIV, Fabul.

Steiner's Break art skills are a reference to the Art of War skills that Knights use in FFTactics.

The Stellazio coins are a reference to the Zodiac stones from FFTactics as well.

The Magic Book optional boss in the Alexandria library is a reference to the book demons from FFV's great library, if you look at the cover of the book, it pictures another type of demon from the game as well.

Atmos the summon was a boss from FFV originally.

The optional boss Hades was a summon in FFVII

One of the earliest ATE events in the Evil Forest involves the Tantalus band playing Rufus' Welcoming March from FFVII

The bells used in Gizolmouke Grotto are a reference to the Bell key item in FFII needed to obtain the Ebot's Fire.

Both Kuja and Xande are motivated by the fear of their own mortality.