An allusion is a literary device used to make a connection between the story or characters to someone or something else known by the reader. Characters can also be aware of the allusion, as is the narrator, Gene Forrester. The most important allusion in A Separate Peace is the one associated with World War II; that is to say, the war is referenced continually throughout the story, so it is the allusion.
The senior class of 1942 at Devon all face being drafted into the war after graduation. The characters know it; they discuss it; and they think about it all through the story. Readers would also know about the history of World War II, and, judging from the story's time period, they would be able to connect with the characters through their own knowledge of the war. This connection helps readers to feel empathy for the boys as they progress towards graduation.
The next part of the allusion is in the title itself--A Separate Peace. The boys are separated from the war and seem to experience a peace separate from world events. The setting outside is peaceful, the school runs on a schedule, and all the boys really need to worry about is school work and graduating.
Ironically, however, there is a war waging inside each of them. Leper must fight the inner conflict with himself, which is the fact that he seems not to fit in anywhere. Phineas fights a physical and mental war after he breaks his leg. For example, Finny must struggle to find his place in life and the war without the strong, invincible body that he was used to. And Gene, the protagonist, fights a war within himself over feelings of jealousy and anger towards his best friend, Gene, and Gene must win his personal battles before he can move on after graduation as well. Hence, the allusion applies to World War II, but also, through the related discussion of peace, connects the characters with the war inside themselves.
Gene eventually remarks about the connection between World War II and the war within himself by the end of the book by saying the following:
"I never killed anybody and I never developed an intense level of hatred for the enemy. Because my war ended before I ever put on a uniform; I was on active duty all my time at school; I killed my enemy there" (204).
Again, Gene is alluding to World War II by making a war reference to his own experiences. And as mentioned above, all of the boys seem to wage an inner war within themselves throughout the novel; so, the on-going reference to World War II is the most important allusion in A Separate Peace.