1958: WEST SIDE STORY over The Music Man
1959: FLOWER DRUM SONG over Redhead
1960: GYPSY over The Sound of Music and Fiorello!
1969: HAIR over 1776
1972: FOLLIES over Two Gentlemen of Verona
1978: ON THE TWENTIETH CENTURY over Ain't Misbehavin'
1982: DREAMGIRLS over Nine
1984: SUNDAY IN THE PARK WITH GEORGE over La Cage aux Folles
1991: MISS SAIGON over The Will Rogers Follies
1998: RAGTIME over The Lion King
1999: PARADE over Fosse
2002: URINETOWN over Thoroughly Modern Millie
2005: THE LIGHT IN THE PIAZZA over Monty Python's Spamalot
As for Avenue Q v. Wicked v. Caroline, or Change, I believe that the musical that deserved to win actually won. I love Into the Woods and The Phantom of the Opera equally and since ITW took Best Book and Best Score, Best Musical deservedly went to PHANTOM.
"I'm just a musical prostitute, my dear." ~ Freddie Mercury