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.
I never actually cried, but I came pretty close when Zelda sealed herself away. Her saying "I'm still your Zelda." and Link's expression... pretty emotional. I'm very surprised I wasn't crying a river, but I was sad when the scene was over, thinking about her sleeping for thousands of years.
I believe the scene at the end of the Earth Temple was very heart tugging.
I didn't cry through the entire game. None of it pulled any heart strings, really. The first thing that came to mind when she was sealed was that she was safe in the back room you couldn't get into from the beginning of the game.
I also kinda figured out that "Grannie" was Impa because of the tear tattoo under her left eye. That kinda took the emotional reunite away for me.
i havent cried, but i have had tears in my eyes for a lot of the parts. ( i do admit i cried when zelda sealed herself away and link pounded on the crystal i was so upset because i thought it looked like link was crying! )