When Orochimaru and Baby Naruto first meet in Chapter 4 on his birthday. Orochimaru reaching into his crib and holding him in his arms as they see each other for the first time. Actually any moment and interaction between the two is bound to be a Heartwarming moment especially in Chapter 13 when they are reunited and become Father and Son.
Anko looking after Naruto despite knowing he is Orochimaru's son. She may hate the man but upon seeing Naruto she becomes a Big Sister figure for him and looks after him.
Haku and Naruto's reunion in Chapter 71, Naruto had been sent into a Heroic B.S.O.D. after believing Haku had been killed when Haku reappears before him Naruto doesn't believe him as he thinks he's a fake. It's only after Haku reminds him of the vow they take when they became Sworn Brothers that Naruto realizes its really him and embraces him and the tears fall out of their and many a reader eyes.
Orochimaru, Tsunade, and Jiraiya being on friendly terms at the end of it. The Three Sannin being together again for the first time in years. Naruto watching notes that if the three put aside their differences they'd be unbeatable.