I'll bite--
50's:
West Side Story should have won over The Music Man (comparing masterpieces though)
Gypsy should have won over Fiorello and The Sound of Music (how many revivals of Fiorello has Broadway encouraged?)
70's:
Purlie has a better score than Applause but never saw it staged so on the fence...
Follies obviously was robbed by Two Gentlemen of Verona (any arguments out there?)
I wish the Candide revival had been eligible-- should have won over Raisin.
80's:
Dreamgirls over Nine-- this is a toughie though. I say Nine's score is better but Dreamgirl's story, characters and production put it in front for me.
Sunday in the Park with George over La Cage aux Folles (which is saying alot since I worked on the original La Cage).
90's:
Once On This Island OR The Secret Garden WAAAY over "The Will Rogers Follies". (Even Miss Saigon is way more worthy, isn't it?)
Jelly's Last Jam over Crazy For You.
Ragtime over The Lion King (great literature over a great show)
Parade over Fosse (though Parade's original production was weak, I agree. Revivals have been awesome though.)
00's:
The Wild Party (1st Choice) OR Aida, OR Marie Christine over the snoozefest called Contact.
Urinetown over Thoroughly Modern Millie.
Wicked over Avenue Q (heresy, I know, but gotta go with my heart here.)
The Light in the Piazza WAAAAAY over Spamalot.
The Drowsy Chaperone over Jersey Boys
Grey Gardens over Spring Awakening (GG is great literature where SA is a good show.)
American Idiot over Memphis (not for the literature but for the greatly moving show).
Wow, from the looks of it, I'm REALLY not happy with the direction the Tony's are headed in. Ok, gang, tell me where I'm wrong :