Maybe a group of rogue ninjas who have been hired by a wealthy and power - hungry lord from a small nation. They see Naruto as a valuable asset and think they can ransom him off to the Hidden Leaf for a large sum of money or use his power for their own gain. Another possibility is a secret organization within the Hidden Leaf itself that has some dark motives and wants to control Naruto for their own ends.
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 new, unknown criminal organization could be behind the kidnapping. They might have heard about Duke's potential and see him as a valuable asset. They could be planning to either brainwash Duke to join them or use his abilities to carry out their illegal activities.
It could be Orochimaru. He has always been interested in Naruto's power and potential. He might kidnap Naruto to try and extract the Nine - Tails' chakra or study his unique Uzumaki bloodline further. Another possibility is a group of rogue ninjas who want to sell Naruto to the highest bidder, thinking his value as a Jinchuriki would make them rich.
One potential kidnapper could be a dark wizard who wants to use Lucy's Celestial Spirit keys for their own dark magic. Another could be a rival guild member who is jealous of Lucy's power and wants to steal her keys to gain an advantage in the magical world. It could also be someone from Lucy's past, like an old acquaintance who has turned bad and has some grudge against her.
It could be a dark organization that has been secretly operating in the shadows. They kidnap Naruto because they believe he has some sort of connection to an ancient prophecy that they want to either fulfill or prevent, depending on their motives.
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.
It could be the Separatists. They might see Anakin as a valuable hostage to use against the Jedi and the Republic. His skills as a Jedi Knight make him a prime target for them to gain some sort of leverage in the war.
It could be a rival family who wants to use Tsuna as a bargaining chip against his own family.
It could be some rogue Hollows who see Ichigo as a big threat and think that by kidnapping him, they can eliminate that threat.
The kidnappers could be a group of hired mercenaries. Some powerful and wealthy person who has something to hide might have hired them. This person could be involved in illegal activities and Castle was on the verge of uncovering the truth, so they order the mercenaries to take Castle out of the picture.
It could be a rival gang. They might see Ponyboy as a threat or a way to get back at his own gang. Another possibility is a deranged fan of his, someone who has an unhealthy obsession and wants to keep him all to themselves. Or it could be a group of criminals who mistake Ponyboy for someone else who has something they want.