Difference of opinion is helpful in religion.
-- Thomas Jefferson
American Religion Data Archive http://www.arda.tm/
The ARDA collects quantitative data sets for the study of American religion. Included are surveys of the general population, selected religious groups, and religious professionals as well as aggregate data files.
Bible Gateway http://www.gospel.com/
Calvin College Post-Reformation Digital Library http://libguides.calvin.edu/prdl Index to digital books covering Post-Reformation/Early Modern Era (16th-18th centuries) theology. Includes both primary and secondary sources.
Christian Classics Ethereal Library http://www.ccel.org/
This is a wonderful resource. Hundreds of full-text classic Christian writings are available.
Dead Sea Scrolls - Library of Congress Exhibit http://www.ibiblio.org/expo/deadsea.scrolls.exhibit/overview.html
The Library's exhibition describes the historical context of the scrolls and the Qumran community from whence they may have originated; it also relates the story of their discovery 2,000 years later.
Papyrological Resources http://www.perseus.tufts.edu/Texts/papyri.html
This page includes links to various data banks of papyri, invaluable resources for research of the New Testament period.
Virtual Religion Index http://virtualreligion.net/vri/
"This index is designed as a tool for students with little time. It analyzes & highlights important content of religion-related websites to speed research."