Like the previously posted Chewbacca Lego mini-figures, there are differences between the Darth Vader mini-figures that I have. I have two Vader mini-figures. One comes from the Final Duel I set (#7200) and the other from the 10 Year Anniversary Darth Vader's Tie Fighter set (#8017) (both sets pictured here). The Final Duel I set was released in 2002, and the Tie Fighter set was released in 2009 and belongs to the episode IV, A New Hope series.
Final Duel I Vader, with Emperor mini-fig.
Tie-fighter Vader on left, Final Duel Vader on right.
The differences between the two Vader mini-figures are readily apparent. There is detail that covers the entire chest on the Tie Fighter Vader, representing his flight suit. The chest of the duel Vader has a 1/2 oval design, covers less of the chest, and has less detail in general. The face of the Tie fighter Vader has two scars, one one the left and one on the right side of his face. The duel Vader has only one scar on the right side of hist face. Additionally, the duel Vader has black eye-brows instead of the grey ones on the tie fighter Vader.