When you shoot a Gossip Stone with an arrow then a green rupee will pop out, reference to the first Zelda game where firing an arrow costs one rupee.
The Kikwi on top of the Great Tree and the Parella that guides you to The Water Dragon, Faron both say "It's a secret to everybody". This is the same thing Rupee-paying Moblins said in the original Zelda.
The Tingle doll.
The ghost hand who appears in the Cawlins Letter sidequest also appeared in Majora's Mask and the Oracle of Ages. In all those games, the hand asks for paper.
Once the Isle of the Goddess fall onto the Sealed Grounds, go under the part that connects the Isle of the Goddess to the Sealed Temple. Look up and in the center of the ceiling you will see the Sages' Medallions from Ocarina of Time.
I've also read that the 3 Dragons are references to the Great Fairies from Ocarina of time, but I don't know how. The three Dragons remind me more of the deities from The Wind Waker.