Thank you, charles, for defending Ain't Misbehavin'. For anyone who doubts its merits as a Best Musical winner, go on youtube and watch the televised version of the original production with the original cast and just watch yourself be proven wrong.
I also want to add that Contact was by far the most deserving winner in 2000. Swing! was fun, but empty, James Joyce's The Dead was boring and The Wild Party, while having flashes of brilliance, was pretentious. All four productions had nearly perfect original casts, but that isn't enough. Contact may not fit the standard mold of a musical, but it was incredible and thrilling. Totally deserved.
In regards to the main subject of this thread, so many, but I'd have to say:
Flower Drum Song over Redhead
Gypsy over Sound of Music/Fiorello
She Loves Me over Hello Dolly (I just don't care for Hello, Dolly)
Seesaw over Raisin
Sunday in the Park with George over La Cage Aux Folles (though I understand La Cage's historical significance at the time)
Into the Woods over Phantom of the Opera
Miss Saigon over Will Rogers' Follies
Smokey Joe's Cafe over Sunset Boulevard
Ragtime over The Lion King
The Full Monty over The Producers
Caroline or Change over Avenue Q
Light in the Piazza over Spamalot
Grey Gardens over Spring Awakening
American Idiot over Memphis
"Sing the words, Patti!!!!" Stephen Sondheim to Patti LuPone.