Heck yeah it made me cry. Once when Zelda and Link were reunited for the first time in the past, and it was super emotional and touching, and then Zelda's Lullaby started playing... Man, I couldn't take it. So many memories of Zelda rushing in at that moment.
I also cried at the end, from pretty much the same phenomenon. Skyward Sword did an awesome job of reminding me just how much Zelda has meant to me over the years. It was a very nostalgic experience.