I realize that it's in nearly all of his works that he does this, but does anyone happen to know in what sections of what books? I understand there's a great critique of Christianity in Human, All Too Human, section I, in places. I'm not talking about his doctrine of the death of God, but rather his critique of Christianity as a social institution.
Here's a website that collects a number of relevant quotes; but as you say, it is really a ubiquitous theme in Nietzsche's corpus-- in fact, Beyond Good and Evil, On the Genealogy of Morals, and The Antichrist consist of little else.
There's also a fair amount of secondary literature on the subject-- you might want to start here, as this will provide context as well as citations.