Iruka is a character that can be greatly affected. Naruto might use his knowledge to make Iruka's life better in the past. The Akatsuki members could also be important in a sense. If Naruto changes the power dynamics early on, their plans and recruitment strategies might be disrupted. And characters like Hinata could have their relationships with Naruto developed in a very different way due to Naruto's time - traveling knowledge and actions.
The Hokage, like Hiruzen Sarutobi, could be significantly affected. Naruto may try to influence his decisions regarding the village and its security. Also, the Uchiha clan members are important. If Naruto aims to prevent the Uchiha massacre, they will be directly affected by his actions. And Jiraiya, as Naruto's mentor, might be influenced by Naruto's new - found knowledge and maturity, which could change their relationship and the training Naruto receives.
Obviously Naruto himself is the most affected. He has to deal with the knowledge of the future and the changes he wants to make. Sasuke is also important. Naruto might try to change Sasuke's path to prevent him from going down the dark road of revenge. Kakashi could be another one. Naruto may share his future knowledge with Kakashi to make him a more effective teacher and ninja.
The Akatsuki would be highly affected. Since Naruto has future knowledge, he could stop their plans before they even start. Also, his friends like Sasuke would be affected as Naruto could prevent Sasuke from going down the wrong path.
In some of these fanfictions, Naruto goes back and tries to save his parents. He might use his knowledge of the future to outwit the enemies that were once too powerful for his family. Also, he could introduce new jutsus earlier in the timeline, which would change the power dynamics in the ninja world. And sometimes, he gets involved in the politics of the village much earlier, trying to make Konoha a more just place from the start.
Obviously, Harry Potter himself is the most common. Since it's about him being thrown back in time, he's the central character. Hermione Granger also often appears, as she's Harry's closest friend and her intelligence would be a great asset in the past. Ron Weasley might also be there, as part of the trio.
If Percy is thrown back in time, his powers could be enhanced. In the past, magic and the power of the gods were more prevalent. The very air might be charged with more divine energy. His ability to communicate with sea creatures could expand, as there could be species that are now extinct or have evolved in his own time. However, he might also face limitations. For example, if he goes back to a time when the gods were at war, some of his powers related to Poseidon might be restricted depending on his father's situation in that war.
The main character affected is Naruto, no doubt. Since he's the one with the Kyuubi being removed. However, the whole village of Konoha could also be considered as affected characters. Naruto has been a key part of the village's defense with the Kyuubi's power. Without it, the village might face new threats and have to adjust their strategies. And other Jinchuriki in the Naruto world might also be affected in terms of how they view their own situations in comparison to Naruto's.
The entire village of Konoha could be highly affected. Naruto, with his second chance, could bring about positive changes in the village much faster. For the younger generation like Shikamaru, Naruto's new approach might inspire them in different ways. And for the older generation, they might be forced to re - evaluate their views on Naruto and the future of the village if he starts making radical changes early on.
Definitely Hermione. Since she's Harry's closest friend and very intelligent, she would be deeply involved in any changes Harry tries to make. Also, Snape. Harry's actions in the past could completely change his relationship with Snape. And of course, Voldemort. If Harry goes back far enough, he could potentially stop Voldemort's transformation into the evil wizard he became.
His close friends like Sasuke and Sakura would likely be among the most affected. They know Naruto well and seeing him in a terrifying state would be very shocking for them. For Sasuke, who has a deep bond with Naruto, it would be especially hard to face a scary Naruto.
Sasuke is definitely one. Since Naruto already knows Sasuke's path in his previous life, he could change Sasuke's fate. Also, Kakashi. Naruto might interact with Kakashi differently, sharing his future knowledge which could impact Kakashi's decisions.
His friends would be affected. They might be both in awe and a bit worried about the new - powered Gaara. His siblings, too. They would need to adjust to this new version of Gaara who has Shukaku back.