Carlos rode for Riis and alongside some dodgy characters, but the way he won that Tour is fairly believable for a clean cyclist (i.e. he had worse days, he had a strong but not superhuman team around him, he had the benefits of being able to sit quietly in the group when people chased Fränk on Hautacam, he kept his powder dry and didn't waste energy, he made his move that won him the race in a place where you would expect a rider of his style to do so - the steepest MTF - and he put in a good but not astounding TT to defend when faced with a shot at the biggest prize of all). I am not willing to state definitively that I think he's clean, but certainly near the bottom of the scale. Ditto for Ryder in the Giro - that was what I believe a clean GT winning performance COULD look like. He had bad days, but others were too weak or too tentative to punish them. He made time on good days, he maximised those areas where he held the advantage and he clung on where he didn't. Then again, though, I'd say Valverde's '09 Vuelta is one of the most believably clean GT wins of recent years too. After all, he was barred from the Tour so was fresher than most of his competitors, Mosquera and Sánchez were injured in the crash in Liège, and most of the time Valverde gained over them came at Xorret del Catí, the first really tough stage after that. He showed weakness (was dropped at La Pandera), and tame racing by others, a strong domestique corps and little time trial mileage helped him.
So maybe it's still a crapshoot.