They might start as antagonists. For example, if a mercenary is hired by a dark wizard to capture Harry Potter, they would directly oppose the main character. But sometimes, they can also be reluctant allies. Maybe they are offered a large sum by Dumbledore to protect Hogwarts and end up working with Harry and his friends.
Mercenaries often interact with the main characters in a transactional way. If they are hired by the Order of Phoenix, they will do what they are paid for, like providing security or intelligence. However, they may not always be completely honest or upfront. Their loyalty can be bought, so the main characters, especially the more idealistic ones like Hermione, may be skeptical of them. There could also be situations where a mercenary has a change of heart during the course of the story and becomes more of a true friend to the main characters rather than just a hired hand.
Definitely Sam and Dean Winchester. They would be like his surrogate brothers or mentors. Then there's Castiel, the angel. He could have some interesting interactions with Harry, perhaps being intrigued by his magic. Bobby Singer could also be there, guiding Harry in the ways of hunting.
They might initially be seen as a threat. For example, if the Cainite have a connection to dark magic, the main characters like Harry, Hermione, and Ron could be suspicious of them.
Obviously Gibbs himself would be a main character interacting with Harry. He'd be like a father figure.
Hermione would surely be one of the main characters interacting with Harry. She would be both intrigued and cautious about his new status. She might help him research and understand the full implications of being the master of death.
Snape would have a very different relationship with Harry in this scenario. Instead of being a constant source of disdain, he might see Harry as an opportunity to shape a Slytherin in a new way. Pansy Parkinson could also be involved. She might initially be against Harry being in Slytherin but later come to accept him, or they could be in a constant battle of wits.
The main characters in 'Harry Potter raised by Winchesters' fanfiction would have some interesting interactions. Harry would surely have a lot of interaction with the Winchesters' enemies as well. Demons and other supernatural beings that the Winchesters fight would see Harry as a new target or a strange addition to the mix. In the wizarding world, Harry might interact with Snape in a more confrontational way, as his upbringing by the Winchesters could make him less patient with Snape's attitude. Also, new characters from the cross - over of the two universes could be created, and Harry would be at the center of those interactions.
I think Harry Potter would definitely cross paths with Tyrion Lannister. Tyrion is known for his intelligence and wit, and Harry's unique perspective from the wizarding world could lead to some great conversations and schemes between them. Harry could also use his magic to help Tyrion in his political struggles within Westeros.
Obviously, Harry would interact a great deal with Newt. But also, they might run into other characters like Hagrid. Hagrid, being the Keeper of Keys and Grounds at Hogwarts and having a great love for magical creatures, would be interested in what Newt and Harry are up to. They could also meet some of Newt's old friends from his adventures in the Fantastic Beasts series.
A Basilisk Animagus could interact with Harry by initially being seen as a threat. Harry, having faced a Basilisk before, would be on high alert. But if the Basilisk Animagus was on the side of good, they could prove their worth by helping Harry fight against Voldemort. For instance, they could use their snake - like senses to detect Death Eaters approaching.
Hermione Granger is a very common character. Since she is Harry's best friend, she would likely be there to help him understand and control his new superpowers. She might research in the library to find out how these powers came about and how to use them effectively. Ron Weasley is also common. He would probably be both in awe and a bit jealous of Harry's new powers at first but would still support him in the end.