I don't know if anyone mentioned these, so I will.
1. If you roll into a tree in Twilight Princess it will often drop money.
2.If you repeatedly attack a chicken in TP, you will eventually switch souls with it (You'll get better, though.)
3. The shopkeeper in Ordon (The one with the cat) has more pictures of her cat than she does of her daughter, 3:1 ratio
4. If you look inside Colin's house, you'll find a drawing of his family with a fourth member (Link?)
5. Midna's theme sounds like Zelda's theme backwards.
That's all I can think of so far.