My favorite has to been in Ocarina of Time where Link and Zelda meet for the first time as kids in her courtyard. I don't know why, but it gave me chills.
There is one scene ever in video game history that has made me cry because of how beautiful it was. That was the scene at the end of Skyward Sword in which Link and Fi say good bye. The monologue that Fi held in that scene was extraordinarily well written, and the music played in the background was so very beautiful. That scene is by far my favourite scene out of all Zelda games.
A lot of the cutscenes in The Wind Waker are pretty comical, most notably the appearance of the Tower of the Gods. I actually laughed when I first saw it.
The scene in Skyward Sword where Groose comes out of completely nowhere… And screws everything up.
That reminds me, I never picked him up from the Sealed Grounds…
And I'm about 10 hours after that point.
I wonder how he survives?
The Dark Interloper scene of Twilight Princess was one that sticks out to me. It was violent, it was creepy and above all, it was AWESOME. The ending of OoT was also well done, what with the courtyard scene and all..
I really like the ending of Wind Waker; it was so sad, yet so epic and still so full of hope. I felt the weight of the history of the series on my shoulders while the King of Red Lions spoke after Ganondorf had been defeated.
"Farewell, this was the only world your ancestors could leave you... please forgive us." </3 Every time :')
I liked when Link drew the Master sword in TP. I also loved opening the gate of time in SS and Link's face when Armoghoma comes back to life in TP The talk between Link and Demise when they are in the sky before the final battle is pretty sweet as well. He sounded so hardcore.