So where have you seen references to Final Fantasy VI? I've noticed a few references in other games.
In Final Fantasy X-2, there's a description of the Ultima Weapon that says not to call him "Atma," obviously a reference to Ultima Weapon being shortened to Atma Weapon in VI.
The summons in Final Fantasy XII are called "Espers", which is not only a reference to VI, but a reference to the American version of VI. Summons in the Japanese version were called "Phantom Beasts" or something along those lines.
Ultros/Orthos makes an appearance as a flan in XII. He will only appear if the three active characters in your party are all female. You get an item from him, and the description of the item says "Don't tease the... flan?" Orthos also appears at the top of the Brightmoon Tor second assent in Final Fantasy Tactics A2.
So yeah. That's all I can think of. :P Anyone else?