Each time you defeat a fiend it will unlock a secret dungeon. There are four of them and they include boss battles from other FF games. Defeat Kraken near the canal by Melmond to unlock Lifespring Grotto. Defeat Lich near the Temple of Chaos to unlock Earthgift Shrine. Defeat Marilith near the Dragon Islands to unlock Hellfire Chasm. Defeat Tiamat in the rivers by the Ice Cave to unlock Whisperwind Cove.
Beat both games to unlock the sound test.
Not really anything special, a reference to Kingdom Hearts. On the 27th Floor of the Whisperwind Cove is a boy in "toy Town" the place with all the houses, in and out The character with blonde hair says, "I've Been having these weird thoughts lately..". Just like the Intro to Kingdom Hearts.
Easter Egg: Link is Dead
When in the town of Elfheim, if you go behind the sanctuary there are 3 gravestones, the one on the left has a message saying "Here Lies Link" which is the hero of the Zelda series.