It's incredibly tough, and I have to mention the two that would round out my top three, Falsettos and Follies, but for me the perfect melding of book and score, humor and emotion, is A Little Night Music. A show that (as I've seen VERY personally) doesn't even need a particularly talented cast to get across just how brilliant it is.
"Why, I make more money than... than... than Calvin Coolidge! PUT TOGETHER!"
~Lina Lamont
My name wasn't, isn't, and will never be Scott.