I think Lance doped. I ask why does it matter? Lets look at the 2009 Tour de France GC standings.
1 Alberto Contador
Got a blood clot in his Brain at age 20. This happens to someone who's in incredible shape training incredibly hard. What could turn someone like this's blood to sludge? Also Lance's teammate. Dirty.
2 Andy Schleck
His brother and teammate admitted to doping. His brother used to be better and then Andy blew by him. Dirty.
3 Lance
He's clean, while training with doping cyclists, beating doping cyclists, being accused regularly of doping, being coached by doping doctors and competing in a sport with a culture of doping. Dirty.
4 Bradley Wiggins
Went from not even a world class time trialer or one day race rider but a world class track rider (i.e. really really good at racing for 4 minutes) into 4th in the Tour de France. Dirty.
5 Frank Schleck
Tested positive.
6 Andres Kloden
Lance and Alberto's teammate. Was on T Mobile. Still Lance's teammate. Dirty.
7 Vincenzo Nibali
Rides for Liquigas, who has a number of superhuman climbers, picked up Basso this year after his doping suspension ran out, and had Beltran test positive and made a big show of how good people they were for kicking him out before his B sample came back, probably because they knew it'd be positive. This was one of their top riders in '09. Dirty.
8 Vande Velde
Vaughters has made a huge show from day 1 of talking about their team's anti doping stance. But Wiggins is clearly dirty. Vande Velde was a former teammate of Armstrong's. Dirty.
9 Kreuziger
See Nibali. Plus he's Eastern European. Dirty.
10 Le Mevel
Relatively unknown, not on a huge time team. Finished 10th with relatively little support compared to the big guns above. Either he's just one needle short of being a super Lance or he's dirty. Dirty.
Autologous blood doping is impossible to test for, so it's impossible to prevent without 24/7 monitoring of cyclists. The good doctors know what the ideal levels are for performance, and it makes the Tour more exciting because people can recover quicker so there aren't dead bodies strewn across the mountain sides every time a top GC contender accidentally over-exerts themselves on a mountain stage the day before two more mountain stages. Only problem is every once in a while a bad doctor messes up and Contador almost dies. Keep enforcing to prevent people from going above and beyond safe doping, and the playing field's level, the races are more exciting and relatively few top level cyclists will get strokes. Everybody wins.