Yes, plenty. LeMond, Evans, Wiggins, Froome, Nibali, even Basso. You could make a case for Sastre too.
There have been plenty of doped riders winning them too, but that was the era the sport was in. If you think the sport remains in that era then I think you'll fit right in over at The Clinic.
It's a terrible answer.
Have there been any clean Grand Tour winners from the last 25 years, and if so, care to name them?