So many moments I love, but if I have to pick, these were the most enjoyable to me.
The Gate of Time/Zelda's Reunion: I know they're two different scenes, but they're close enough together
When watching the Gate of Time assemble itself in the Sealed Temple, it looked so beautiful and astounding. To me the Gate of Time actually looks somewhat futuristic and like it belongs in another time, especially in the temple which shows its age. I always love watching this scene, so pretty~
The other scene with Zelda reuniting with Link...it has so much emotion in it. You learn of so much, and just seeing Link himself be so shocked and upset(almost to the point of crying) really made the scene and the plot for me.
I also loved all the expressions on the characters. Especially Link's, since he goes from very adorable when he smiles to extremely cool and tough when about to fight someone like Ghirahim. =D