In the church's library area, the first room's backmost shelves have 2 secret rooms. As was mentioned above, one has a chest containing a Church Amplifier item for Cleric that makes Church skills do 1.5x increased damage and also contains a photo of a family (maybe the Pontiff's?), and the second room contains a chest that gives you a Shield Tome. It teaches whoever you give it to the Shield skill, which costs... 50% HP, SP, and TP to use (current values, not max), and gives all your allies Perfect Defense. It activates with +30 speed, meaning it's quite likely the first skill to activate in a round. I'd recommend giving it to someone who doesn't really use their skills all that much, like Cleric; outside of Boost All and healing, Cleric doesn't really do much in my fights, and whenever she runs out of SP I can just have Demon use the share SP skill.
Many thanks to all the other people here who posted about secrets and hidden things that they found; I, for one, would never have learned about the Collar if it wasn't mentioned.