I was actually just thinking about this the other day. The answer I came up with was there is no possible way to pick just one as my all time favorite. Here is my best try.
Rent
It was the first musical that I ever even really heard of. Rent was really my first and will alway have a very special place for me.
Evita
Hairspray
Follies
Bare
Sweeney Todd
Company <----- Company actually has my favorite song of all time (Being Alive)
Gypsy
The Last 5 Years
Martin Guerre
Ragtime
Sunset Boulevard
[Title of Show]
Wicked
The Wedding Singer
So there is my top 15 in no order at all
"I'd rater be nine peoples favorite thing, than a hundred peoples ninth favorite thing"