The irony of obscurantism
Nietzsche presents obscurantism as a force not to darken individual thoughts, but to reopen the discourse for a less arrogant, less assumptive philosophy. This means that the "darkening" philosophy is necessary to approximate the truth. It's ironic that intentionally darkening the field might lead to a more enlightened discourse.
The irony of love in Christianity
Nietzsche maintains in the aphorism called, "Love" that love as is commonly understood was a construct offered by Christianity, which though it has created much beauty, also serves to provide a limiting moral scope and an environment wherein Christianity can prey on those who want "love" but don't get it from the people who matter. This is ironic because it means that the Christian concept of love is actually responsible for feelings of rejection and frustration because of its idealistic expectations.
The irony of Pilate and Christ
Nietzsche explicitly states this irony in the passage about Pilate, where he praises Pilate's skeptical questions, "What is truth?" and heralds him as the hero of the Christian passion. This is ironic because he's cast as the antagonist in the passion sequence and is in the Christian creed as the agency of Christ's crucifixion.
The irony of skepticism
Nietzsche's tendencies for skepticism are at the root of his philosophy, but they turn ironically against himself. If one should reject systems of philosophy wholesale, it's difficult to avoid self-defeating arguments. This irony is explored in the section, "Knowing how to clean oneself," where Nietzsche says that it is primarily important to move toward the truth, even if it means cleaning yourself in dirty waters. He's pointing to the inherent inadequacies in his own work, but claiming that it's better than any other options.
The irony of morality
Since Nietzsche doesn't subscribe to any beliefs in a transcendent natural law or divine law, he has to view morality as a system built by those it constrains. This is inherently ironic, because everyone needs to subscribe to an abstract "good-for-the-community" morality, meaning that the only people who don't abide by the rule are "immoral" for being self-centered. But that's the same system that traditional morality uses, leading to a chicken-egg paradox about which came first, the construction or the construct.
