I don't know how underrated it is, but I fell completely in love with the score to Fanny after the Encores! concert and am disappointed it's not more well known.
Shows that have already been mentioned that I would agree with are pacific Overtures, Parade (my current obsession) and She Loves Me. I do think Parade and She Loves Me have certainly gotten recognition for their incredible scores, but they can always get more.
I would also suggest I Do! I Do! and 1776. I think both have good scores, but there are some gems in both that don't seem to be as appreciated as they should be. ("My Cup Runneth Over" is, in my opinion, one of the most lovely and romantic songs in musical theatre history.)
When I see the phrase "the ____ estate", I imagine a vast mansion in the country full of monocled men and high-collared women receiving letters about productions across the country and doing spit-takes at whatever they contain.
-Kad