It could be a rival detective agency. They might be jealous of the Hardys' success and kidnap them to try and get an edge in the detective business. They could hold the Hardys hostage until they give up some of their secrets or cases.
Maybe a group of criminals that the Hardys have been chasing. They're tired of being on the run and decide to take matters into their own hands by kidnapping the boys. This group could be led by a mastermind criminal who has a personal grudge against the Hardys.
Another plot could involve a personal vendetta. Perhaps someone from their past, who they put in jail or wronged in some way, is out for revenge. So they kidnap Frank and Joe to make them pay. It could be a character who has been biding their time and finally sees an opportunity to strike when the Hardys are in a vulnerable position.
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.
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.
The Grimm could also be involved in an unusual way. Perhaps a new type of Grimm that has the intelligence to kidnap. They might be working with a human or Faunus villain who has some sort of control over them, and they take the character to an unknown location where the RWBY team has to face not only the Grimm but also the mastermind behind it.
It could be a jealous rival of the spirit animals' owners. This person might be envious of the special bond and powers that come with having a spirit animal and decides to kidnap them to spite the owners.
A secret society that believes Mycroft is a threat to their hidden agendas. They may think that by kidnapping him, they can stop him from interfering with their plans. They would likely be very well - organized and have resources to keep him hidden.
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.
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.
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.