Fallen Kingdom brought an emotional impact. By the end, you care that this kingdom has come to ruin and that the entire village has been slaughtered.
Gods Don't Bleed was amazing in terms of directing, and made not only Herobrine, but pretty much every mob shown into a complete badass.
And Cube Land upgraded him from badass to completely friggen' terrifying. Even if he did get his rear handed to him by a pig in the end, the whole thing was still very impressive.
In a different and more obscure direction, Minecraft Transitions showed me, when I was just getting into this stuff, that a landscape made of blocks can indeed be utterly breathtaking.
If someone makes something that can tie the best of those together, I will pretty much explode with sheer happiness.
Those are my top minecraft videos. You?