I know millions of references.

Lindblum weapon shop: Cloud

Mount Gulug: Mount Gulg/Gurgu Volcano from FF1 and the music is similar as well

Flare Star is from FF6

Rei's Wind is from Tactics

Unusual/Strange/Beautiful potion say something about Matoya.

Holy bell: Says something from Minu/Mindu/Ming-Wu

The Hero Story is about Josef's death.

There are tons more. I'll post them later maybe.