The Sound of Music - To this day whenever I watch the movie or see it on stage, hearing the entire chorus of nuns singing amazing harmony in "Climb Every Mountain" while the family leaves everything familiar to them behind to flee the Nazi's and start over gives me chills every time.
The King and I - It is so heart wrenching to see this amazing, loving man say his final words to all his children, and especially Anna who, by this time, is madly in love with him. It always makes me cry, and I think it's masterfully written.
Cabaret - Never have I been this depressed and inspired and completely speechless after a musical. I'm talking about the revival staging, certainly not the original. I wasn't ready to let go and actually applaud for the actors because I was still in awe of the show's beauty and amazingly staged finale.
Nine - It brought tears to my eyes every time the music would swell, Little Guido taking the gun from Guido, and then all the women in their lives (atleast in the revival,) come down the staircase for the last time to kiss, hug, and essentially "thank" Little Guido for saving his older self's life. Whenever the mother would embrace him, I would sometimes literally start sobbing. And finally, as the cast assembled themselves on the circular staircase and as they hold out the dim, mysterious last note, Louisa enters and Guido turns to her - and the audience knows everything between them is going to be alright. It was brilliant.
Others that come to mind, but no where near as perfect as the above, are Into the Woods, Sunday in the Park with George, Gypsy, Rent, Fiddler on the Roof, Brigadoon, Bare, Peter Pan, and South Pacific.
"If you are going to do something, do it well. And leave something witchy."
-Charlie Manson