You don't like second person because at first it seems as though the text is telling you what you think, what you feel. But then you look down at your hands, down at the book being cradled in your fingers, and you recognize that second person narrative is just another form of suspension of disbelief. If you let yourself realize that the narrator is not you, but is actually you, then you can enjoy the story without any preconceived notion of what you would and wouldn't do in the situation. Once you get there, you cease struggling with the idea that you did whatever the book tells you that you did, and instead look into the story that unfolds because of what you did.
To get past all of that second person nonsense, I would recommend reading Jay McInerney's Bright Lights, Big City. Best use of second person I've read. Someone else mentioned Calvo's If on a winter's night, a traveler already, but while it's an interesting story it's quite experimental, which means that sometimes the issues you may encounter while reading actually have nothing to do with the second person itself and everything to do with the fact that it's just off the wall compared to standard prose, heh.
No. Second person very rarely works in prose because it eliminates the entire character building part. It's very lazy writing. Why bother creating a character with flaws and believable traits when you can write action and slap 'you' into the narrative?
I never even liked the pick your own adventure books, and as I got older, I began to suspect that the second person narration might have been why.
Like ~CrazyAce01, I think Choose Your Own Adventure books are the main place where second person is actually expected. There's no reason you couldn't write those as "If you want Dave to do X, turn to Y," or "What should I do? [Some options follow]," but since you're already getting the reader involved in the plot, you may as well go that final step and make the book about them.
Outside of that particular sort of book, I think it's one of those things that's a bit like a strong spice: best in small amounts, and not at all in most things. Then again, there will be those few things where it's good to have a lot of it. I'm not familiar with Homestuck, but in this analogy it might be a bit like a curry: it benefits from having lots of second person spice.