Characters who seem mis-sorted

They address this issue in Book 2. The sorting hat will allow a person to choose the house they want. It tried to steer Harry into Slytherin, but he had already decided that he wanted to be in Gryffindor.

It's mentioned again in book 5, during one of the DA meetings (when Hermione gives out coins that have been enchanted with the Protean Charm).

So, the Sorting Hat will offer you its opinion, but ultimately the witch or wizard chooses their house, even if it's a poor fit. For instance, we know that Pettigrew likes to ally himself with the most powerful person he can find, and as Gryffindors are supposed to be brave, he probably had some idealized version of himself in mind when he put the Sorting Hat on, and despite whatever the hat told him, he was probably insistent on being in Gryffindor, so it allowed him to join.

Ah I had thought the sorting hat only lets you choose if he's torn but that might be my misunderstanding. And I guess Percy would want to be in Gryffindor like his parents and brothers. And Crabbe and Goyle would see Slytherin as the house for winners. But I wonder why Hermione would favour Gryffindor over Ravenclaw or even Hufflepuff.

Well, I think she is more Gryffindor than Ravenclaw. I mean she was the one who suggested the notion of Dumbledore's Army and she broke school rules quite regularly. In any case, in the fifth book, Hermione does say that the sorting hat was torn between putting her in Ravenclaw or Gryffindor but chose to put her in Gryffindor. I would say she probably has more Gryffindor in her than Ravenclaw.

Most of that seems to come later on though, ie a good while after she was sorted. Particularly in the first book, Hermione seems to be there to get good grades and stay out of trouble. It only seems to be after she's saved from the troll that she becomes more open to bending the rules and even then she worries about getting caught.

In Book 3, she has the time turner but uses it solely to do more classes (very Ravenclaw). She doesn't even tell Harry about it, let alone suggest using it to help their cause, until Dumbledore gives her the nod to do so.

I suppose the Sorting Hat knew she had it in her to be a good Gryffindor, but I think it odd that if it was so torn, Hermione's own preference would have been Gryffindor over Ravenclaw. Surely someone whose main ambition was to be thought of as smart would love to be in the house of smarty pants?

Hermione seems to feel that bravery is more important than intelligence though (she tells Harry so in the first book, before he's off to meet Quirrel on his own), which is very much a typical Gryffindor trait. But there's no doubt that she could have been a good Ravenclaw too...

Intelligence and purity.

Hermione seems to feel that bravery is more important than intelligence though (she tells Harry so in the first book, before he's off to meet Quirrel on his own)
Good point, I'd forgotten about that.

Well if I remember correctly, in the first book while on the train, Hermione mentions something about Gryffindor sounding the best out the houses and that Dumbledore had been in Gryffindor. But by her comment in OOTP, it did sound that the sorting hat made the decision by itself instead of Hermione's comment. Besides, I think the sorting hat sees traits in people beyond the present. It didn't take Hermione all that long to get into rule breaking.

Fair points. I guess all four examples fall apart then!