A big one is malaria. Daniel Headrick's The Tools of Empire covers this at some length, but the gist of it is that before the advent of prophylactic use of quinine to prevent malaria, it was relatively difficult for Europeans to penetrate far into the interior of Africa. They mostly stuck to their coastal forts, away from the mosquitoes (not that they necessarily knew that it was mosquitoes causing the disease) that would surely kill them. This was also true in parts of India, though British control there was much more established by the nineteenth century. The Scramble for Africa, Headrick contends, was largely facilitated by the advent of industrially produced quinine and steam engines.

Another example is actually in British North America, specifically the Virginia Colony. Colonists in Virginia, Maryland, and the Carolinas died in alarming numbers upon first coming over. Only if they survived something they called "the seasoning" could they expect to live beyond a few months. If I recall correctly no one is precisely sure what "the seasoning" was, but it involved flu-like symptoms and may have been typhus. In any case, the mortality rates in 17th-century Virginia were quite high, and it is not unreasonable to think that if the native population had not already been weakened by their own problems that they might have resisted English encroachment due to this disease.

A source for that is Edmund Morgan's American Slavery, American Freedom.