Naruto vs. Pein was pretty badass... before he flipped his shit and they did bad cg for the Pein vs Kyuubi-naruto portion, that was just ugly.
I love Naruto vs. Kaguya. Kaguya was a Goddess, and she fought Naruto seriously after seeing that he was a true threat, and Sasuke wasn't. She even took him to a dimension away from Sasuke and he fought her as an equal, spamming moves that require so much Chakra, only Bijuu, and the likes of Madara, Hashirama, and Kaguya would have the Chakra to use.
Of course his fight with Kaguya was after he had been fighting for days, split his Chakra hundreds of times over, gave his and Kuramas Chakra to an entire fucking army *a process where naruto had to give more of his own Chakra than Kuramas, to act as a buffer*