I just wondered what religious institutions were doing during the Civil War era, and I realized that I didn't know where to look and that I don't really know the history after the puritans and before the religious right.
All religions, or specific religious movements?
I've been out of the field for some time, but when I did religious history I always appreciated Mark Noll's book for general reference. It's readable, reasonably comprehensive, and well researched.
Martin Marty's Pilgrims in Their Own Land: 500 Years of Religion in America is getting old, but it is still a very readable and enjoyable history.