The irony of romance
The teenagers' relationship to one another is a romantic relationship, or at least it has the potential to develop into one. The relationship between the apparitions to one another is also romantic, but in a nasty, dangerous way that causes serious tragedies. The irony here is that the human need for love drives some of the most destructive behavior on the planet.
The irony of time
The first irony of time is the obvious one, that even though the flow of time causes changes, the essential makeup of a human being is the same, meaning that Ned views the past not as an alien, foreign land, but as an experience of one kind with his own experience. True change is accomplished privately, but the questions that plague us are the same through time.
The irony of religion
Religion serves a major role in the novel's plot line, but it's not reinforced by a moralistic, legalistic perspective. Ironically, the novel serves as an indication of a path toward ascension, not driven by desire, but by charity. When Ned is forced to climb a terrifying mountain that has already hurt him before, it's his desire for Melanie's good, not his own, that leads him to victory.
The irony of community
Ned's success hinges on his willingness to work with others toward a common goal. By uniting his journey with the journey of his father, they find success, whereas if they were alone, they might fail. This is ironic because it goes against a primal instinct to be private and isolated whenever emotional things are happening in life.
The irony of success and failure
The irony of success is that if you're focused on getting what you want, you won't get it. This comes through beautifully in the novel, because the suitors are dead-set (literally) on getting what they want and having victory over each other, but Ned's selflessness makes him successful.
