This prompt from Long and Short Reviews initially made me respond "Every one of them." I think studying English literature at school was a great way to ruin a decent book. (It says something that when I read "To Kill a Mockingbird" under my own steam I liked it, but my friends who had to read it for class hated every word.)
I did, however, come up with three in particular.
Joby - Stan Barstow. According to Amazon this book is supposed to be full of working class themes, but all I remember is being forced to read this book aloud paragraph by paragraph by people who were giggling at the mention of breasts.
The Charlie Barber Treatment - Carole Lloyd. For me this was one of those books the librarian tries to push off on you because it had "meaning", since it deals with a boy who finds love after his mother dies. We did at least finish this one, unlike "Joby", but I found it dreary as hell.
Lord of the Flies - William Golding. This is one I think I might have liked had I not had to read it down to the millimetre. I can remember getting a good mark for an essay comparing Simon and Roger as good and evil. That said, the fact that the plot hinges on using a pair of myopia glasses to make fire - which you can't actually do; you need long-sighted glasses - did rather ruin it for me.
So which books were ruined for you?