David Epstein does a marvellous job of highlighting the problems, and potential solutions, in his TED talk titled "Are athletes really getting faster, better, stronger? (here). The author of The Sports Gene presents a series of illustrative examples. One example illustrates the impact of technology on cycling performances. A graphic from his TED talk is reproduced below. In the 24 years after 1972 the record for distance travelled on a bike in one hour increased by almost 5 miles. However, when the rules were changed to require that the same equipment be used, the improvement shrunk to less that 1,000 feet.
Sometimes the comparisons are more interesting to statisticians than sports fans. In 2006 the Journal of Sports Economics published a paper that sought to make comparisons across all the competitions that go to make up the Tour de France. They started by soliciting the opinions of cycling experts on the relative importance of winning the various jerseys on offer (Yellow, Green, Red Polka Dot) and podium finishes (stage win, second place, third place). Using the relative importance derived as a result of this survey of opinions, they ranked the cyclists using data for the period 1953-2004. Bernard Hinault headed the ranking. In joint second place were Lance Armstrong and Eddy Merckx.
In 2006, when the paper was published, Armstrong held the record for the most Yellow jerseys (6). Armstrong was not one of the five cyclists that competed in the virtual race in The King of Mont Ventoux. However, he does feature prominently in the stage won by Marco Pantani. The speed which the two climb during the last 10 minutes of the 2000 Mont Ventoux stage is astonishing (here). It was a battle between the 1999 Yellow Jersey (Armstrong) and the 1998 Yellow Jersey (Pantani). Pantani won the battle (Stage win) but Armstrong won the war (Yellow Jersey).
What happened since that epic battle raises further issues about comparability. Pantani died in 2004 at the age of 34 - having had his run in with the doping authorities. He is still listed as the winner of the 1998 Tour de France. Armstrong has been stripped of all his wins - having eventually admitted to doping. No winners are listed for the Tour de France for the years 1999 to 2006. Armstrong has been stripped of the 1999 to 2005 wins, and Floyd Landis of his 2006 win, for doping. Nobody was subsequently promoted to Yellow for this years. By contrast, Andy Schleck was deemed to be the winner in 2010 after Alberto Contador was found to have doped.
While the comparisons are interesting as thought experiments, it is probably best to remember that the winners are the best at that moment in time. Even those who subsequently get promoted would probably agree that it is not the same as being deemed the "best" competitor at the time.