Several battle shonen series have used their friendship tropes to get even the vilest villain to join the happy-go-lucky, main character's side. While turning anime villains into heroes has become the norm for most shonen series', few have utilized the trope as widely and effectively as Naruto.
With a protagonist who struggled with feelings of loneliness, insecurity, inadequacy, and a literal demon, Naruto is a series all about pulling the best of people from even the darkest of places. It's a series about forgiveness and redemption; and over its long run, it has told the redemption story of several villains.
Zabuza Momochi
Zabuza Momochi was one of the series' first, big villains; and despite only being in the story for a relatively short time, he still told an effective and endearing redemption story. Zabuza had a survival-of-the-fittest upbringing in the Hidden Mist Village and a leadership style that bluntly acknowledged his own underlings as disposable.
As much as he wanted to maintain that tough exterior, Zabuza secretly and unintentionally had a soft spot for his faithful partner, Haku. After Haku's death, Zabuza eventually gave in to Naruto's friendship speeches and decided to avenge Haku, fending off an army of bandits in one of Naruto's most iconic scenes.
Neji Hyuga
Neji Hyuga during his worst days wasn't anywhere near as bad as some of the series' most dastardly villains, but that doesn't mean he was exactly nice during his introduction. As part of a lower sect of the Hyuga Clan, Neji felt as a child that he was limited by his own background, and that fostered feelings of inferiority and resentment against his own family, particularly Hinata.
This made him cold and abusive towards her and even unforgiving towards his own teammates. It wasn't until his epic confrontation with Naruto during the Chunin Exams that he'd finally see the error of his ways. Since then, Neji did a lot to show his support for Naruto, his friends, and the rest of the Hyuga Clan. After the Fourth Great Ninja War, some Neji fans may argue that he might've done a little too much.
Kabuto Yakushi
The definition of an identity crisis, Kabuto was an orphan who lost all of his memories after a head injury, a spy who, in Danzo's attempt to get rid of chief members of Root, killed his own den mother, and a secret agent for Orochimaru that was turned into a secret agent for the Akatsuki but was turned back into a secret agent for Orochimaru.
On top of being a leading goon for all of those villainous organizations, Kabuto also became a main conspirator for the Fourth Great Ninja War during his own attempt to find himself. After finally learning to accept himself for who he was, Kabuto sided with Naruto's friends during the latter half of the war and, in the aftermath, became the director of his old orphanage.
Itachi Uchiha
Itachi Uchiha walked a thin, grey line that was stained a little redder than a few fans may care to admit. While the early story had fans believe that Itachi ruthlessly slaughtered his clan for no reason, he was actually trying to protect his little brother and the greater good of Konoha. After discovering that the Uchiha Clan was planning a coup, Itachi was conflicted on whether or not to fight his own family.
When the village gave him an ultimatum and after stumbling upon Madara's own plot, Itachi decided to kill his clan to at least save his own brother while still working his way into the Akatsuki as a spy. Though choosing the lesser of two evils still had him do despicable things, Itachi was always working towards the bigger picture and cared deeply for his little brother.
Obito Uchiha
Obito Uchiha was a lot like Naruto when he was young. He was spirited, ambitious, and cared deeply for his friends and village. Unfortunately, the harshness of the Third Shinobi World War challenged his ideals and eventually killed him. After Madara resurrected him, Obito sided with his plans to create a world without war and became one of Madara's lead agents/conspirators.
In turn, this led to a lot of conflict and murder under his own leadership and him literally becoming the Ten-Tails. After realizing that he was just a pawn in a greater conspiracy, Obito helps Naruto's team in the end and even sacrifices himself to save his best friend, Kakashi, one last time.
Nagato/Pain
Nagato was one of the originators of the Akatsuki who initially led the group to help and protect disenfranchised victims of battle. However, as part of Madara's evil machinations, he turned to the dark side and used the Akatsuki to create peace by any means necessary.
Besides leading an evil version of the Akatsuki, Nagato also became pretty infamous for singlehandedly (literally) destroying Konoha and killing countless lives. He'd eventually repent for his sins after a cathartic fight with Naruto and resurrected everyone he had killed during his attack, passing off his legacy of peace towards Naruto.
Orochimaru
Though he never quite apologized for his crimes against Konoha and, well, humanity, Orochimaru still managed to redeem himself throughout the story, subsequently becoming one of Naruto's most beloved villains. More than a ninja, Orochimaru is a scientist who aspired to gain all knowledge and conducted several, inhumane experiments to find a way to live long enough to do so which led to his exile from Konoha which led to his vengeance plot against them.
During the events of the Fourth Great Ninja War, Sasuke's own plans to create peace and save Konoha swayed Orochimaru and encouraged him to fight alongside the very ninja he had betrayed before. In the aftermath, he had a truce with the Kage, reestablished Otogakure, and created an entire community of synthetic humans.
Madara Uchiha
Not counting Kaguya, Madara Uchiha was the big villain of the original series. Corrupted by war and feeling betrayed by his own village, Madara conspired to a decades-spanning plot to force peace upon the world. Doing so had him manipulate a terrorist cell, arrange the murder of countless people, and the inevitable backfire of trying to use mind control to save the world.
After seeing his plan's downfall, Madara finally admits defeat to Hasirama Senji, not just as an opponent but as a leader trying to create the peaceful world that they both dreamt of when they were kids.
Sasuke Uchiha
Sasuke has one of the most fascinating character arcs in Naruto. Overcome by his own ambitions and bloodlust against his own brother, Sasuke defected from Konoha and became a principal agent under Orochimaru. He'd later join the Akatsuki, fight all of the five Kage at once, and help start the Fourth Great Ninja War.
His journey to redemption had him confront the dark underbelly of both criminal organizations and his own, home village; but in the end, he realized that more violence doesn't create peace. In grand, cathartic fashion, he fights alongside Naruto in their epic battle against Obito, Madara, and Kaguya and, in the ensuing years, became a respected ninja and leader within Konoha.
Gaara
Gaara's redemption arc was one of the most fulfilling of the early series. When he debuted, he stalked the Chunin Exams as a cold, ruthless killer and an unstoppable monster prey only to his own anxieties and immaturity. He was instrumental in Orochimaru and the Sand Village's attack against Konoha and wreaked havoc as the infamous One-Tailed Beast.
Though most saw him as just a pure monster, Naruto, a tailed-beast host himself, connected with how lonely and angry Gaara felt and, in one of Naruto's nicest acts of kindness, tried to show Gaara that he had a friend. This would work wonders since Gaara and his siblings not only became key allies to the village afterward, but he also became the proud Kazekage of the Hidden Sand Village.