I never have been able to settle on a favorite Jerry Herman score, and I don't think I ever will. I love them all!
If I had to choose his top three though, they'd be:
(In no particular order)
Mame, Mack and Mabel, and The Grand Tour/La Cage Aux Folles.
I cheated a little bit, but it's too hard to choose. La Cage and The Grand Tour are both so elegant and beautiful. All of his scores are, really.
"Light the candles! Get the ice out! Roll the rug up, it's today!"