Lack of Parents
Most of the character is this novel either have never met their parents or don't know who their real parents are. This idea of being totally alone seems to be the central theme of the book. To begin with, Homer is an orphan. He attaches himself to Dr. Larch by making himself useful and demonstrating great promise in the medical field. Lacking traditional authority figures, Homer grows up to make questionable moral decisions no the least of which is having a baby with a woman and then telling her husband they adopted it from St. Cloud's. Similarly, Candy and Wally don't have parents in the picture either, although little is known about their childhoods. They first appear when they come to Dr. Larch seeking an abortion. They're headstrong kids who get in too deep. Finally, Angel has a unique situation of not knowing his real father very well. Although as a family friend, Homer is a part of Angel's life, the boy doesn't know that Homer is his real dad. All of these characters or somewhat transient and impulsive, not having been tied down to traditional authority structures.
Deception
Perhaps representative of this lack of authority, the characters all do their fair share of lying. Each believes they have substantially acceptable motivations for the deception, however. For example, Dr. Larch keeps it a secret from his orphans that he performs abortions. He cannot allow the children to know how narrowly they escaped death by possessing that knowledge. He's also somewhat ashamed for his practice since he's morally opposed to abortion in most situations, but he's often dealing with girls who are victims of rape and incest. After hearing about the horrors of unlicensed abortion clinics, he silently takes up the practice in order to save the girls from certain trauma and possible death. Regardless, Homer is devastated to learn that he's been lied to all these years. It takes him years to move past the initial hurt. Homer invents his own critical lie in his private life. After Candy has a baby with him, they both are shocked when Wally returns home having been injured instead of killed in the war. Attempting to spare Wally the insult, Homer and Candy decide to tell everyone that the baby is adopted. Behind his back, Homer and Candy continue to have an affair for fifteen years afterwards. In fact the deception, though everyone is aware of it, is never outright talked about, so Homer never receives closure regarding Angel.
Abandonment
No doubt stemming from Irving's own childhood, he writes a great deal about abandonment. In this book it's a consistent theme throughout the text. The obvious example is Dr. Larch's running of an orphanage. Unwilling to start his own family, he provides a safe growing environment for kids without families. He does not, however, mentor or "parent" the kids because he refuses to be emotionally vulnerable with them. After they graduate, they're on their own. All of these kids have been put up for adoption by young mothers who were not prepared to raise children on their own or in whatever circumstances they find themselves. Kids like Homer grow up feeling unwanted which seems to be propagated in their children as well. Homer's son Angel grows up thinking he is an orphan because of a lie. In fact he's never given the opportunity to know Homer well. Once Wally returns, Homer relinquishes his claim to fatherhood and turns his attention to Dr. Larch's medical practice. Although Angel doesn't know his true parentage, he still senses the strange dynamic between his three parental figures.