Well, the other students in Gryffindor would likely be a bit taken aback at first. But then, knowing Hermione's intelligence and her tendency to be different, they would probably accept it. They might be curious about how she's going to manage to keep up the charade. The Hufflepuffs would be generally kind and understanding, perhaps even offering to help her if she needs it. The Ravenclaws would be intrigued by the idea and might study her transformation from a more academic perspective. The Slytherins, as a whole, would be more likely to try and use her disguise against her, either by blackmailing her or trying to expose her in a way that would cause her and her friends embarrassment.
The plot could be that Hermione dresses as a boy to help Harry and Ron in a situation where they need a male - only presence. For instance, they are trying to get information from a group of pure - blood male wizards who are very traditional and would not talk to a girl. Hermione, being the intelligent and resourceful witch she is, decides to disguise herself as a boy. She then has to act the part, learning the mannerisms of boys. Along the way, she might start to understand the male perspective a bit more, and this could also lead to some self - discovery for her. Plus, when the boys she's interacting with finally find out she's a girl, it would surely cause quite a stir.
The boy might be confused at first. He may not understand why he is being dressed differently from other boys he sees. For example, if he goes to school in a dress, his classmates might stare or make comments, which could make him feel self - conscious.
Harry would probably be very confused at first. He knows Hermione is usually so studious and responsible. He'd likely try to talk to her to find out why she did it. Ron, on the other hand, might be a bit more blustery. He'd probably say something like 'Hermione, what were you thinking?' and be quite shocked. The professors would be disappointed and would likely call her in for a stern talking - to, as Hermione has always been a model student.
Ron would probably be extremely confused and might make some awkward jokes at first. But once he sees that Harry is doing it for Ginny and that it's all in good fun, he would likely come around and support it. Hermione, on the other hand, would be more accepting from the start. She might even offer some advice on how to make the cross - dressing more believable, like using magic to adjust Harry's voice to be more feminine. The other Gryffindor students would likely have a range of reactions, from laughter and amusement to those who are a bit more conservative and might be a bit taken aback at first.
The Twilight characters would be quite shocked. Vampires like Edward might be very suspicious of Hermione's new status as an imprinted character. Werewolves like Jacob would have a different reaction. Since imprinting is a big part of their culture, they might be more accepting but also cautious as Hermione is an outsider from a different fictional universe. They would need to figure out how to incorporate her into their pack or deal with her in some way.
Harry would be crushed. He'd feel like he lost a sister. Ron would be in total despair, probably blaming himself. Ginny would be heartbroken too as Hermione was like a sister to her. The Weasley family, who had accepted Hermione as one of their own, would be in mourning. They'd all wonder how they could have prevented it and would be angry at the unfairness of it all.
Harry would be extremely worried. He'd probably rush to her side immediately and try to do whatever he can to help. He might blame himself for not being there to protect her. Ron, on the other hand, would be in a state of shock at first and then would try to use his humor to lighten the situation a bit while still being very concerned. Hagrid would be devastated. He sees Hermione as one of his students he cares about, and he'd likely bring some sort of magical creature - related remedy, thinking it could help.
Kakashi would likely be amused by the whole situation. He might give Naruto some tips on how to blend in better as a girl, using his own knowledge of disguise techniques. Iruka would be more concerned about the reasons behind Naruto dressing as a girl and would make sure Naruto is comfortable with it. He would also be there to support Naruto if any of the other villagers had a negative reaction.
Hermione would probably be defiant at first. She's not one to take injustice lying down.
She might initially be shocked and scared. But then she would start to think rationally and try to find a way to outwit Snape. For example, she could start to gather evidence against Snape's own wrongdoings, if there are any, so that she can turn the tables on him.