The Invincible is named after the airship from FFIII but even more amusing, it's design shares many similarities with Amano's concept artwork for the Enterprise
586px-FFIV_-_Amano_Enterprise.jpg vs. Ffix_invincible.jpg
A further connection to FFIV is that fact the Invincible fulfills the same role as the Lunar Whale in FFIX by being a ship capable of traveling between the two worlds.
The Iifa Trees Theme is actually based off of FFIV's Another Moon Theme
Also, the Crystal World Theme is a remix of Prelude, the reason being, that Prelude is often the theme used when characters encounter the crystals in the early FFs like FFIV.
FFIX has a hidden mini-game much like the matching game in FFII unlocked by screwing with the Snow Sled and other NES games. At the end of the game when Prelude is playing and The End appears, if you put in a certain button combination, you can play Blackjack.
The Treasure Hunter Rank is a reference to FFTactics, where you could also raise your Treasure Hunter Rank by doing Propositions, and collecting FF artifacts.
Gilgamesh, known as the Four Armed Man in the game also makes a sly reference to Locke Cole of VI by being associated with the Treasure Hunter Quest and calling himself a great Treasure Hunter but he's also a blatant thief in the game. :ffvipatpat: