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.
One of the characters most likely to be affected is Dumbledore. Harry going back in time could change Dumbledore's plans and strategies against the dark forces. Ron would also be affected as he is Harry's other best friend. Their friendship might develop differently if Harry changes things in the past. And then there's Hagrid. Harry might be able to help Hagrid in ways that he couldn't in the original timeline, perhaps by preventing Hagrid from getting into certain troubles.
His father's friends, the Marauders, are very likely to interact with Harry if he goes back in time. He could become a part of their group, learn their secrets, and even participate in some of their pranks. Hagrid is another character. Harry has always had a special bond with Hagrid, and going back in time, he could strengthen that bond even more. And of course, Snape. Harry could try to change their relationship from the start and understand Snape better.
Hermione is another common character. Since she is always so intelligent and resourceful, Harry might turn to her for help in understanding the implications of time travel. They could work together to change certain events, like preventing the release of some dark magic that they later had to face. And of course, Ron would also be around. His loyalty and friendship would be a source of support for Harry as he navigates this new timeline.
Neville Longbottom can also be a main character in some 'Harry Potter goes back in time' fanfictions. Given his growth and importance in the original series, in the fanfic, Harry might go back and help Neville become more confident earlier. This could have a significant impact on the fight against Voldemort as Neville could then be an even more powerful ally from an earlier time.
Harry himself is obviously a very popular character in these fanfictions as he is the one being sent back in time. But also, characters like Sirius Black are often popular. Fans like to explore how Sirius would react to Harry being in the past, and how their relationship could develop differently.
Definitely Harry himself. Since he is the one being sent back in time, he is central to the story. His actions and decisions in the past are what drive the plot forward.
Hermione is often one of the most common characters. Since she's Harry's best friend and very intelligent, she's likely to be involved in any time - traveling adventures. Another is Dumbledore. Harry might seek his guidance in the past, and Dumbledore's wisdom would be invaluable. Also, Sirius Black could be a character Harry interacts with, especially if he wants to change the events that led to Sirius' death.
Definitely Hagrid. Hagrid has always been around Hogwarts and has a connection to the students. Sirius could interact with Hagrid if he goes back in time. Maybe Hagrid could help Sirius in some way, like providing shelter or information. And Bellatrix Lestrange could also be in the picture. Since she is part of the Black family, Sirius might have to deal with her in the past, either to try to change her or to stop her from doing something evil.
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.
Obviously, Harry Potter and Sirius Black are the main characters. Harry is the time - traveler, and Sirius becomes his mate in this new timeline. Other characters like Dumbledore are likely to also play important roles, as he is always involved in matters related to Harry and the greater good of the wizarding world.
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.