Naruto defeating Menma/Tobi by using the Flying Thunder God Rasengan that his father, Minato had used in his fight against Tobi during the Kyuubi attack. Made even greater by the fact that Naruto was wearing the Fourth Hokage's cloak. A new instance of Naruto being Just Like That Hero.
The Akatsuki of all people pulling a Big Damn Heroes by helping Naruto take on the Masked Man. For so long the Akatsuki have been the overseeing villains of Naruto, but to see them come in and actually be allies was epic to watch.
It seems that no matter which reality Naruto is in, Itachi still makes his enemies flee in fear.
Just the fact that the Akatsuki are good guys, Kishimoto personally had a hand in the production as well as the ending song being done by the guys who did the second ending is pretty awesome indeed.
Sakura's father pulling an Offscreen Moment of Awesome by taking Minato's place in the alternate world as the Fourth Hokage and the village's hero.
Naruto and the Kyuubi/ Kurama actually truly teaming up for the first time and leading to the Kyuubi actually fully materializing.
Even though they were fakes, seeing the Konoha 12 take on the Akatsuki as a team is very cool to watch, especially with Gai and Kakashi backing them up. It shows how far these characters have grown over the years as they can hold their own against some of the most dangerous nins in the Nations.