I don't know that I actually cried, but I got very emotional, especially at the end.
Firstly when Zelda sealed herself away
Secondly when I was about to go defeat Demise and Fi said "Remember, Master, I will always be with you"
Thirdly when Fi and the Master Sword were sealed away. At this point I realized, no matter how annoying Fi had been, that I loved her and was gonna miss her so much. When she said "This emotion...I think they call it...happiness" I swore she was gonna say love, but it was still sweet. I was so sad when she had to go though.
I was super upset when I started Hero Mode and Fi didn't remember me...