Well, Kraven the Hunter is a very possible kidnapper. He loves the hunt and Peter would be the ultimate prey for him. He might want to prove that he can capture and defeat Spider - Man. Shocker is also a likely candidate. His vibro - shock gauntlets could be used to subdue Peter and kidnap him. There's also the possibility of a new villain created specifically for the fanfiction, someone who has a personal grudge against Peter for some reason, like a scientist whose experiment Peter accidentally ruined and now wants revenge by kidnapping him.
In kidnapped Peter Parker fanfiction, the Kingpin is very likely to be a kidnapper. He has the resources and the power to organize such a thing. He might want to use Peter to gain an edge in his criminal activities or to send a message to other superheroes. Electro could also be a kidnapper. He could use his powers to abduct Peter and then try to drain his powers or something similar. And don't forget about Mysterio. He could stage a fake kidnapping but then it turns into a real and dangerous situation for Peter.
The Green Goblin is a likely kidnapper. He's always had a vendetta against Spider - Man. Also, Doctor Octopus could be a candidate. His mechanical arms and his intelligence make him a formidable foe who might kidnap Peter for his own devious experiments. Another one could be the Vulture, who might see Peter as a valuable asset to sell to the highest bidder in the criminal underworld.
It could be some disgruntled former employees of Stark Industries. They might feel that they were wronged by Tony in some way, like being fired or not getting the credit they deserved for their work. And they see kidnapping him as a way to get revenge. Peter might just be collateral damage since he is associated with Tony.
One group that could be the kidnappers are AIM (Advanced Idea Mechanics). They're always interested in getting their hands on advanced technology, and Stark has plenty of that. The Ten Rings terrorist organization is also a possibility. They've targeted Stark before and kidnapping him again would be a way to make a big statement. And let's not forget some rogue elements within S.H.I.E.L.D. who might think that Stark is a threat and kidnap him to keep him in check.
There could also be a group of villains working together to kidnap Sonic. For instance, a combination of Eggman and some of his more powerful robot creations along with a couple of other villains from Sonic's rogues gallery. They might have a grand plan that requires Sonic's capture, like using his power to open a portal to a world full of chaos energy that they can then control.
A jealous rival of Inuyasha might kidnap Kagome. For example, another demon who wants Inuyasha for himself might think that by taking Kagome, he can get Inuyasha to do his bidding. This would create a lot of drama and conflict between Inuyasha and the kidnapper.
It could be a rival team's coach or a jealous player. They might see Kuroko as a threat to their success and decide to kidnap her to keep her out of important games. For example, if there's a big championship coming up and they know Kuroko's skills are crucial for her team's victory.
Enemies from her past, such as old villains she's fought against, would be likely kidnappers. They might hold a grudge for her previous defeats and want to use her for revenge or some dark purpose.
The Naraku would be a likely kidnapper. He is always plotting against Inuyasha and trying to get his hands on the Tessaiga. Kidnapping Inuyasha would be a way for him to either steal the sword or find a way to break Inuyasha's spirit so that he can no longer oppose him.
The Joker is a likely kidnapper. He has a history of causing chaos and targeting the Bat - family. He might see kidnapping Batgirl as a way to get back at Batman or just for his own twisted amusement.
In certain fanfictions, a jealous rival of Amy Rose could be the kidnapper. This could be another female character who has feelings for Sonic and sees Amy Rose as a threat. She might think that by getting rid of Amy Rose, she can have Sonic all to herself. Or it could be a character from Amy Rose's past who has some unresolved issues with her and decides to kidnap her to get revenge or make her pay for something that happened a long time ago.
The Yiga Clan could be likely kidnappers. They've always been enemies of Link and would love to get their hands on him. They might see kidnapping him as a way to stop him from interfering in their plans. Another possibility is the Gerudo thieves. Although not all Gerudo are bad, there could be a group of them who think Link has something valuable and decide to take him hostage.