Two unambiguous testaments to the military aspect of the invasions of the Americas.
In Peru, one of the burials in a sixteenth-century cemetery outside of Lima appears to be the oldest skeletal evidence of a gunshot victim in the Americas. Other burials in the group may also show gunshot evidence as well as injuries from maces (a traditionally Andean weapon). A lack of grave goods and other contextual evidence suggests a hasty burial, though not a mass grave pit.
The arquebus was an initial shock weapon in encounters between Spaniards and Native Americans, but it is generally considered less important than the more numerous crossbows, steel swords, and the all-important horses. In Mexico, arquebus or cannon would break-up infantry attacks, and could be used to impress locals. But time and again, Spanish battle chronicles follow a similar pattern. After initial contact (sometimes involving trickery or ambush), the Spaniards and their allies would fight the Aztecs or other Mexicans primarily on foot, inflicting damage but loosing fighters. Eventually the mounted horsemen would get into the fray, ride down the natives, and then get into the back area of the opposing army and wreak havoc with their lances. This decided many more battles than firearms did.
The following video from National Geographic (one of the sponsors of the research), shows some of the evidence
Some seventy years later, the English brought their arms to the coasts of Virginia, and recently armor and arms have been recovered from Jamestown. While iconic and impressive, as the article notes, these had been put away when famine, not natives, brought the English to their knees.
Update: More skeletal evidence of the Spanish conquest of Peru