The First Amendment Center maintains an online library, which includes a searchable database of court cases dealing with the religion clauses of the First Amendment.
The Library of Congress had made the Congressional Journals kept in both the House and the Senate available online. The journals can be searched or browsed to locate notes pertaining to the debates surrounding the First Amendment.
The Library of Congress has created a web guide for the Bill of Rights with links to a several historical documents. Included are letters from and between Thomas Jefferson and James Madison.