There are several themes in this book. One of the predominant ones is growing up in the middle of a war. These boys are just that--boys--and they are preparing to be sent into a war that they didn't start or didn't ask for. A time in their lives that should be filled with sports, girls, school and having fun is brutally destroyed by this war.
More specific to the story of Gene and Finny is the theme of friendship and equality. What make a good friend, and can two people who don't consider themselves equally be friends? Would a true friend really intentionally hurt his friend?
Also, as the enotes page says, another theme is guilt and innocence. How should, if at all, Gene be punished? Did Finny deserve what happened to him? Who's to decide guilt and innocence?