Naruto has plenty, which is a given considering it is a Shonen manga. The end of the Sasuke Retrieval Arc, the Hunt for Itachi arc and the Pein Invasion Arc are the most well known.
WARNING: Here there be spoilers. If it's been aired on the free version of Crunchyroll, the spoiler will not be tagged as such.
One of the first wham chapters was the chunin exam arc, when Orochimaru join the exam. At first he pretended to be a very blood thirsty woman, who scared the shit out of Sakura and Sasuke. His appearance turned a relatively serious arc, frightening.
After Sasuke was able find courage and fought Orochimaru off, lightening him up in a fiery explosion. Orochimaru just laughs it off and bit Sasuke on the neck.
When Sasuke woke up from the Cursed Mark, his power and sadism was beyond anything Sasuke had shown before and was frightening.
When team 8 met Gaara. His power and ease of murder made him as scary as OROCHIMARU.
Kabuto turned out to be working for Orochimaru was very shocking. At that point, Kabuto was just a nice guy.
Sasuke and Gaara's fight was made of this. With Sasuke showing off his Chidori. And then Gaara transforming into the One-Tails.
Orochimaru revealing to have replaced the Kazekage and fought the Third was a huge one. Especially as he revealed the Edo Tensei and the Living Corpse Reincarnation
The next wham came from the Sasuke Retrieval arc, when Sasuke willing left Konoha.
Then Sasuke woke up from his coma, he had a new super mode.
The Naruto and Sasuke fight, had both of going through power ups like crazy, with each unlocking their super modes. And Sasuke actually getting away.
The Kazekage Rescue arc had one when Gaara died.
The Sasuke and Sai arc had Naruto releasing the Fourth Tailed form. Naruto had become a monster and nearly killed Sakura.
Or the fact Sai's mission was to kill Sasuke and that Danzo was working with Orochimaru.
The Hunt for Itachi had quite a bit of whams. One of the biggest was Jiraiya's death and that Itachi was a good guy deep down.
Pain when on a rampage killing hundreds of named characters, including Kakashi.
He finished the rampage by making Konoha a crater.
Naruto returning and actually being a match for Pain.
But that is sadly turned as the Tendo Path beat Naruto and Hinata tried to save him, and it ended in her near death. Causing Naruto to enter the 6 tailed form.
Pain is able to beat the 6 tailed form, forcing Naruto into the eighth tailed form. As Yamato sees that Naruto is able to enter the Ninth tailed form.
As Naruto is about to release the seal, the FOURTH HOKAGE stops him.
The Confining the Jinchūriki arc had a few whams. One of the biggest was Naruto met his mother Kushina.
His mother was the Nine-Tailed jinchūriki before Naruto and that Tobi was the cause of the Nine tailed fox's attack on Konoha were pretty big whams.
Kabuto coming back and knowing Edo Tensei turned some heads.
The War Arc has the biggest one with chapter 559: spoiler: The real Madara is dead and resurrected as an Edo Tensei, the one we thought was Madara is put in question. A lot of people saw it coming, but even more didn't.
Some may have seen it coming, but unless one of the known characters is a deity of deception, Tobi is an entirely unknown character. Either way, we have no freaking clue and practically no way to theorise about the identity. WHAM! The only known possibility is that Tobi could be Uchiha Obito (both only had the Sharingan in their right eye) but this is unlikely because there is reasonably good evidence to indicate that Obito is dead.
Then it turns out that the sharingan eye that Tobi has is, in fact, Obito's. And, as for chapter 599, it has finally been confirmed that Tobi was Obito all along. This is easily the biggest Wham Episode all together, as the Driving Question of the entire series has finally been answered.
Chapter 618: Orochimaru has negated the Death God Seal, summoning all four deceased Hokage. And while they Came Back Wrong, they're at full strength this time.
Chapter 627: After listening to Hashirama's story on the Uchiha and Senju clans' feud, how the village came to be, and pretty much getting all the answers he was looking for, Sasuke decided he'll take the battlefield...AGAINST Madara. That's right. Sasuke finally is back to the good guys' side. Not only that, but Taka is now fully reunited, Orochimaru is taking part on the war, along with the FOUR HOKAGES.
Chapter 629: Rin was the jinchuriki for the Three-Tails! The Mist kidnapped her and sealed the tailed beast inside of her, so that when she was rescued they would be able to use it to destroy Konoha. Her death at Kakashi's hand was actually a Heroic Sacrifice to protect the village!
Chapter 630: Minato arrives on the battlefield
Chapter 631: Sasuke declares that he's going to become Hokage.
Chapter 632: Sakura can use Tsunade's Hyakugou no Jutsu. "Next time look at my back," indeed.
Chapter 637: Madara's elaborate plan backfired spectacularly and Tobi is now the Jinchuuriki of the Ten Tails.
Chapter 660: Madara has extracted Kurama, the Nine Tails from Naruto.
Chapter 663: Madara has become the third Sage of Six Paths after absorbing the Shinju.
Chapter 664: Black Zetsu was able to steal the other half of Kurama and Madara comes bursting in.
Chapter 665: Obito betrays Madara.
Chapter 667: Kabuto joins the fray as a good guy, having realized his true nature after being trapped in Itachi's Izanami, and is helping to revive Sasuke. Meanwhile, Might Guy enters Gate Mode, expecting to use the 8th gate and die in his fight with Madara.
Chapter 670: Naruto meets Hagoromo, the Sage of the Six Paths, who tells him that he is is the Sage's younger son reincarnated.
Chapter 671: Naruto is not only confirmed to be the Sage's younger son reincarnated, but that Sasuke is the Sage's older son reincarnated. Not only that, but they're not the first reincarnations — in fact, the reincarnations of the previous generation are confirmed to be Hashirama and Madara respectively. Meanwhile, Naruto and Sasuke are about to gain the powers of all nine tailed beasts, who Obito restored to Naruto after betraying Madara.
Chapter 674: Madara steals Kakashi's Sharingan, enters the Kamui dimension and attacks Sakura, with Obito too weak to do anything as he's trying to hold off Black Zetsu. As such Naruto and Sasuke can't do anything to stop him.
Chapter 675: Naruto manages to restore Kakashi's eye. Meanwhile, it turns out that Madara mind-controlled the Hidden Mist and orchestrated the events leading to Rin's death, up to and including Kakashi being the one to kill her, in order to get Obito under his control.
Chapter 676: Infinite Tsukuyomi begins to take effect.
Chapter 677: Due to the Infinite Tsukuyomi, only the original Team 7 and the edo tensei Hokages are still conscious. Also, Yamato was inside Spiral Zetsu.
Chapter 678: Black Zetsu literally backstabs Madara, revealing that he is not his will, but Princess Kaguya's, making her The Man Behind the Man to everyone.
Chapter 679: Kaguya regenerates her body by way of Madara's own by hijacking Madara's use of God: Nativity of a World of Trees.
Chapter 681: Kaguya starts crying, being reminded of her two sons by Naruto and Sasuke. It's then revealed that Kaguya is also part of the Juubi, and was sealed away by her two sons in order to stop it. However, before she was sealed away, she created Black Zetsu to act in her place and revive her. To do that, Black Zetsu proceeded to cause the start of nearly every conflict in ninja history by manipulating Indra into attacking his brother Ashura, starting the Uchiha-Senju feud. From there, he continued to watch over both brothers' successors until he found someone who could awaken Rinnegan: Madara. Since the very beginning, the world itself has been his Unwitting Pawns, this entire war being orchestrated just for the sole purpose of reviving Kaguya.