It depends a bit on how you define alternate history. Is it still alternate history if the major events are the same, but lots of the details change? Also, does it count if it's in another world, but it's basically our history with the serial numbers filed off? Here are some suggestions:
Colonial Gothic - American Colonial period with magic in the background
7th Sea - Swashbuckling adventure game with some magic, basically set in Europe but with different country names. Swashbuckling Adventures is the D20 version
Hollow Earth Expeditions - Pulp adventure inside a hollow earth, otherwise similar to our early 20th century
Spirit of the Century - Pulp Supers, basically historic, but encourages making changes to history for the sake of the game
Tour of Darkness - Savage Worlds Vietnam era plot point campaign
Weird War II - D20 Modern alternate history World War II
Shadowrun - effectively alternate history, given that it was written some time ago and the events it predicted did not occur ;-)