This is always a hard question... I try to make this list all the time and it is always changing, but here's my latest attempt, in no particular order
RAGTIME (thrilled to see this on so many lists)
ONCE ON THIS ISLAND (my favorite of all time)
MERRILY WE ROLL ALONG (my favorite Sondheim)
OLIVER
WEST SIDE STORY
1776
MY FAIR LADY
INTO THE WOODS
THE SECRET GARDEN
ANNIE
I realize that this list is a mix of shows that have great scores and shows that mean a lot to me. Having said that, though, I do think the scores of both "Annie" and "The Secret Garden" are underrated. "Annie" gets mired in the popularity of "Tomorrow" when the rest of the score is ignored. "The Secret Garden" all I can say is that I've been listening to the CD for 16 years and never tire of it.
There are also scores that I acknowledge as great, such as SWEENEY TODD, but I prefer to SEE that show as opposed to listening to it.
The Ahrens & Flaherty website