I can't believe you all missed the biggest one in the whole game.
It's called "Final Fantasy." That's like the ultimate reference.

Just kidding, calm down. But you did miss some.
FF1: The key item Rat Tail is a reference to the Cave of Ordeals in FF1 when Bahamut asks you to find it in order to prove your courage.
In the description of most of the key items needed to make the Supersoft, there is a reference to Matoya from FF1.

FF3: Not really a reference, but moogles originated in FF3.

FF4: This is probably an FF8 reference, but the attack Darkside could also be a reference to Dark Knight Cecil's special command, called "Dark Wave" in the Japanese version. Only difference is that Dark Wave hits all enemies, and Darkside only hits one.
The Rat Tail made another appearance here, as an item you could trade for Adamant.
The Antlion in FF4 was supposedly tame, yet attacked Prince Edward anyway. In 9, he attacks Prince Puck.

FF5: There's a card called Boco in FF9, referencing Bartz's chocobo.
The Airship card has the sprite of the airship from FF5. Or 4. They both look the same.

FF7: Kupo Nuts. Come on, guys. The Mog House mini-game?
The moogles' "kupo" sound effect is the EXACT same one. Not even joking.
After Alexandria is destroyed, one of the Pluto Knights is talking to a flower girl near the ruined steeple. If you talk to the flower girl, she'll say "He's nice, but isn't much for personality." Remind you of another flower girl and lacking-in-personality soldier?

FF8: Beatrix's Save the Queen was Quistis's ultimate weapon. It was also used in Tactics.
Quina's Eat command. Though the effect is different, it's the same command as Devour in FF8.
The spell naming system (Fire, Fira, Firaga) was the same as in 8. Actually, it was the same in almost all the Japanese FF games.

FFT: The Stellazio coins in 9 are named after the Zodiac. Tactics was the first RPG (I think) to include these. There's even a 13th Stellazio, although not Serpentarius.
The Auto-Potion support ability.
A lot of Steiner's Sword Art abilities (Mental Break, Armor Break, etc.)

There are some references to the GameBoy Final Fantasy games as well, including bosses from the Final Fantasy Legend games and something specialFind it yourself. from Final Fantasy Adventure.

SaGa Frontier 2: Did Gustave have something to do with the construction of Lindblum and Alexandria? Like his homecity in SaGa Frontier 2, Hahn Nova, Lindblum has three sectors: Industrial, Business, and Theatre. Think "Blacksmith", "Shopping", and "Entertainment". Similarly, take a look at Alexandria from the world map. The castle sits in the center of the lake, with three segments of the town divided by rivers. Hahn Nova has a very similar setup: The castle in the center of town and roads seperating three sectors of town. Probably a coincidence, but interesting nonetheless.

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 on PE. In addition, when you first enter 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.