I heard this exclamation today and it hit me for the first time: what an odd juxtaposition. Of all the things in the world that are unlikely to be holy, crap would have to be near the top of the list. I’ve spent some number of years studying religion and many a Sunday in church, and I have yet to ever come across anything even remotely like consecrated poo.
Hmmm. Well, maybe The Purpose Driven Life.
I guess “holy cow” would also be a strange juxtaposition, but I always just assumed that this phrase was making fun of Hinduism.
Gently Hew Stone 
I’ve heard some stuff in Sunday School that could be considered “Holy Crap”. I wish people would stick to doctrine.