I never quite understood the disconnect between the Klingon appearance in the original series and the others (TNG and beyond) until I read recently on Wikipedia:
A canonical explanation for the change [in Klingon appearance] was given in a two-part storyline on Star Trek: Enterprise. The two episodes, "Affliction" and "Divergence", aired in February 2005. An earlier story arc featured the Augments, genetically-engineered humans left over from the Eugenics Wars of the late 20th century, and who were defeated by Captain Jonathan Archer and the Enterprise in Klingon space. The Klingon High Council fears that Starfleet was developing armies of Augments; after gaining access to genetic material from the Augments, the Klingons perform experiments to increase their own intellect and strength. The experiments turn disastrous when a flu strain mutates and becomes a deadly plague that spreads across the Empire, causing physical changes resulting in the afflicted bearing a TOS-era appearance. Dr. Phlox of the Enterprise formulates a cure for the virus, but the physical alterations remain in the populace and are inherited by offspring. Phlox indicated that "someday" the physical alterations could be reversed.
But in the TNG episode "Rightful Heir," the cloned Kahless has the same appearance as the "mutated" Klingons. Kahless lived long before the experiment in the canonical explanation. Is this a plot discontinuity?