Back in the old days they knew how to cheat

1904: The original winner was Maurice Garin, however he was found to have caught a train for part of the event and was disqualified.

1996: Bjarne Riis has admitted to the use of doping during the 1996 Tour. The Tour de France organizers have stated they no longer consider him to be the winner, although Union Cycliste Internationale has so far refused to change the official status due to the amount of time passed since his win. Jan Ullrich was placed second.
1999-2005: these races were originally won by Lance armstrong, but in 2012 his wins in the tour de france were removed due to doping violations.
2006: Floyd Landis was the initial winner but subsequently rubbed out due to a failed drug test.
2010: Alberto Contador was the initial winner of the 2010 event, but after a prolonged drug investigation he was stripped of his win in 2012.