It could be a group of rogue Death Eaters who want to use baby Harry as a bargaining chip against Voldemort. They might think that by having Harry, they can gain power within the dark wizard's ranks or even overthrow him.
The potential kidnappers could be a cult within the wizarding world. They might believe that Harry has some sort of divine or special magical essence as a baby that they can harness for their own dark and twisted purposes. Or it could be a wizard who has lost his own child and in his grief - stricken state, kidnaps Harry thinking he can replace his lost loved one.
Maybe some jealous wizards who are envious of the attention Harry is getting even as a baby. They figure if they kidnap him, they can disrupt the prophecy and gain the spotlight for themselves. Another possibility is that it could be a group of wizards from a different magical society who believe Harry has special powers that could benefit their own society, so they take him as a baby.
The potential kidnappers could be a secret society within the wizarding world that has its own agenda. They might believe that Hermione has a special power or connection that could either help or harm their cause, so they took her at birth to control that. It could also be a non - human magical being, like a centaur or a goblin, who thought that Hermione's birth was a sign of something significant in the magical world. They kidnapped her to study her or use her in their own cultural or magical practices. Or perhaps it was a wizard who had a grudge against Hermione's parents and took their child as revenge.
It could be a rogue vampire who wants Bella for her unique blood. There are many vampires in the Twilight world who might be tempted by her smell. Another potential kidnapper could be a vengeful werewolf who blames Bella for something, perhaps for the way the vampires and werewolves' relationship has changed. It might also be a human who has somehow found out about the vampire world and thinks they can use Bella to gain power or knowledge.
It could be a group of rogue demigods who are jealous of Percy's status and power. They might think that by kidnapping and torturing him, they can gain some of his abilities or just to prove that they are stronger.
The Sith could be potential kidnappers. They might see Princess Leia as a powerful Force - user and want to either turn her to the dark side or use her in some dark ritual. Another possibility is the bounty hunters. They could be hired by some powerful and shadowy figure to kidnap Leia for various reasons, like for political leverage or to get information from her. Also, a new and unknown alien race that has just entered the galactic scene could be the kidnappers. They might not understand the significance of Leia but kidnap her out of curiosity or because they misinterpret her actions as a threat.
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.
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.
It could be a rival vampire clan. They might see the son as a threat because of his unique nature, being part human and part vampire. They may think that as he grows up, he could become very powerful and pose a danger to their own power and territory in the vampire world.
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.
The kidnapper could be an estranged family member of Beckett. There might be some family feud or inheritance issue that leads them to believe that by kidnapping the baby, they can gain an upper hand. Or it could be a completely random person who has a mental disorder and randomly targeted Beckett and the baby because they saw them as an easy target.
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.