Your characters are your babies, your darlings, your best friends and yet when you think of them in this respect that is when you lose real characters and interesting plot lines.
Stephen King says in his book, On Writing, "Try anything you like, no matter how boringly normal or outrageous. If it works, fine. If it doesn't, toss it out. Toss it even if you love it. Sir Arthur Quiller-Couch once said, "Murder your darlings," and he was right."
The goal of any book is to use your characters for some overarching purpose, whether a moral or a lesson or even just an impression of something. This means that everything has to go wrong for characters until the end when they have attained the victory they have sought since the beginning (unless of course this is a tragedy).
What ways can you "murder your darlings" without actually killing them off?