The three spirits that watch over Hyrule are a reference to the goddesses in The Legend Of Zelda: Ocarina Of Time. Their names are similar.

In the house in the Fishing Hole, there are pictures on the wall. The one on the far left is that of the fisherman from The Legend Of Zelda: Ocarina Of Time.

The songs that are played during the game (for example, the hidden skills and when you call for your horse or summon a bird), are the songs that you play in Zelda: Ocarina Of Time.

When wearing the Zora Armor, if you look closely, The Zora Sapphire is used as a brooch on the armor.