I'm not sure these are really the top 3, but they're my favorites:
1. The Phantom of the Opera
2. My Fair Lady
3. Maybe Les Miz or Sweeney Todd or Fiddler on the Roof or Carousel or Camelot or 1776 -- I'm not sure I can pick a #3.
Believe it or not, I haven't seen Wicked, so that may become #3, based on what I've heard about it.
Audrey, the Phantom Phanatic, who nonetheless would rather be Jean Valjean, who knew how to make lemonade out of lemons.