It's hard to choose only one. I really like the opening of the Door of Time, when you jump with Epona in Gerudo Valley and in the End Credits, see Mido and King Zora sad for their losses. Also, in the End Credits, when all the Sages appear.
I was really stunned by the preface chinematics. It is really well done with smooth and natural movments, and most importantly; it sets the mood of the game and engages the player in the story. Simply put: It leaves a great first impression, and gives the player a reason to play through the game.
OoT would not have been what it is today without that introduction.
I know it's just this little itty bitty moment - not even super important - but when you meet the Deku Tree Sprout. It's so...hopeful, I guess, haha. Though it might just be a rush from defeating your first temple.