It refers to the comparison of two similar objects or concepts. Conversely, the phone "apples to oranges" descibes the comparison of two different and unequal things.
It means there has been no change. You`re trading apples for apples, there`s nothing new.
There is "small choice in rotten apples" because all the apples are rotten and, therefore, you will have a rotten apple no matter which one you pick.
It means decayed, spoiled or decomposed. Also foul, bad smelling and used in another way it can mean corrupt dishonest or bad.
Throw them away that is what you can do with them!