Church Archives
GENERAL & REGIONAL - all denominations:
Overview of Church Records Research from the Wisconsin Historical Society
Religion and the Founding of the American Republic from the Library of Congress has a good historical overview of religion in early America.
BAPTIST
American Baptist Historical Society
Baptist History & Heritage Society
Southern Baptist Historical Library and Archives
CATHOLIC
Genealogical Resources & Services of St. Mary's Seminary & University - St. Mary's was the earliest large Catholic settlement in Maryland and the families there pioneered early to places like Ohio, Kentucky, Southwest Pennsylvania etc. taking their religion with them.
Local Catholic Church and Family History & Genealogical Research Guide
CONGREGATIONALIST
Congregational Christian Historical Society - the protestant puritan movement that settled New England became known as Congregationalists. If you had a New England minister in your family or a later Congregationalist minister check here at their large database of obits for clergy and missionaries
CHURCH OF THE NAZARENE
Church of the Nazarene Archives
LUTHERAN
Evangelical Lutheran Church in America: Archives
METHODIST
United Methodist General Commission on Archives & History
MORAVIAN
Moravian Archives from the Moravian Historical Society
PENTECOSTAL
Assembly of God: Flower Pentecostal Heritage Center
International Pentecostal Holiness Church Archives
PRESBYTERIAN
Presbyterian Historical Society of Philadelphia collects, preserves and tells the story of the American Presbyterian experience.
QUAKER
Digital Quaker Collection from Earlham School of Religion