Maybe a group of outcast ninjas who have a grudge against the Uzumaki clan. Since Naruto is an Uzumaki, they might see kidnapping him as a way to get revenge on the clan. They could be jealous of the Uzumaki's power and reputation and want to use Naruto to bring the clan down.
The Akatsuki is also a possibility. They are after jinchuriki, and if they knew about Naruto's existence as a baby, they might try to kidnap him early. They could think that by having him from the start, they can better control the Nine - Tailed Fox within him.
It could be a group of rogue shinobi from a neighboring village who are jealous of Konoha's power and see Hinata as a valuable hostage. They might think that by kidnapping her, they can gain some leverage over Konoha in terms of resources or territory.
It could be a rival ninja clan if this is in a ninja - themed story. They might see Sakura as a valuable asset to get information about her own clan or to use her skills against her people.
One possible kidnapper could be a rival engineer who is jealous of MacGyver's fame and ability to solve problems so effortlessly. This person might think that by kidnapping MacGyver, he can steal his ideas and take credit for his inventions. Also, it could be a group of eco - terrorists who believe MacGyver's work has been harmful to the environment in some way and want to force him to make amends by using his skills for their cause. A third option is a deranged fan who has an unhealthy obsession with MacGyver and wants to keep him all to himself, thinking that kidnapping is the only way to have MacGyver's undivided attention.
Perhaps a dark guild that has been observing Fairy Tail for a long time. They see Mirajane as a valuable asset and believe that her powers can help them in their evil plans. So they plot to kidnap her and force her to cooperate.
Perhaps an old enemy of Igneel, Natsu's dragon father. They might see Natsu as a way to get revenge on Igneel. They think that by torturing Natsu, they can somehow hurt Igneel even though he's not around. Or it could be a group that is after the secrets of dragon slayer magic and believe Natsu has the key to unlocking those secrets.
Another possibility is some disgruntled former employees. Maybe they feel they were wronged by Stark and want to get revenge. They know his routines and weaknesses well enough to plan a successful kidnapping.
Some disgruntled members of the Sand Village itself could be the kidnappers. Maybe they feel that Temari or her family has wronged them in some way. They could kidnap her in an act of revenge. This would add an interesting layer of complexity to the story as it would involve internal village politics and betrayal.
The Akatsuki could be potential kidnappers. They are always on the lookout for powerful jinchuriki like Naruto to extract the tailed beasts from them. Orochimaru could also be a kidnapper as he is always interested in obtaining powerful bodies and Naruto's strength would be very appealing to him.
A powerful and vengeful warlord from a forgotten realm could be a kidnapper. He might see Wonder Woman as a threat to his plans of conquest and decides to take her out of the picture by kidnapping her.
Perhaps it's a group of bandits who don't really understand who Mikasa is. They just see her as a valuable hostage to get what they want from the military or the local communities. They might be after food, weapons, or just a large sum of money in exchange for her safe return.