What was Ayu's third wish?
The simple answer is that we don't know. 

However, in Episode 24, Shiori makes a guess (based on a feeling) of it being, "I want my dearest person to always be smiling."


   "For that to happen, everyone around that person has to be having a happy life, too." Which brings her to the conclusion that such a wish triggered all the miracles happening around Yuuichi, such as all the girls getting better, including Ayu herself.