Everyone has most likely heard of the fabled cocoa beans and apples of dungeons, maybe you have even found some. But why can't there be an easier way to obtain these precious foodstuffs? Apples can heal 2 food-bar as well as being crafted into the fabled golden apple. Cocoa beans are for delicious cookies and brown wool (for the artists). I propose that these should be farmable!
Apples can be crafted into into seeds (similar to 1.9 update pumpkins). This or either when eaten they leave a core that can be crafted into seeds. (I haven't thought about how the farmable crop would work out, like textures and what not).
Cocoa beans could be planted just like seeds. The crop would look similar to a giant melon/pumpkin stalk. When fully grown it the crop's boughs could be dappled with brown speckles.