For me it's the death of Daphnes Nohansen Hyrule. The look he gives Link after putting him in a bubble-thingie. It's full of relief and sadness... Then you just see him disappear while floating away.
I voted for the Deku Butler's Son simply because the idea of someone losing a child has always really gotten to me. No parent wants to outlive their child, and the idea that someone would have to makes me really sad. I don't know, that's just me. I blubber like an idiot whenever I hear those sad songs about someone's kid growing up. It's just always been a soft spot for me, so that part of MM really tugs at the old heartstrings.