One similarity between both Salinger and Holden is their preoccupation with young people. Salinger was an author who found his audience with the young and felt that within young people was a voice of incorruptibility that could appreciate what he was saying. Holden's belief of himself as "the catcher in the rye" stems from his embrace of young people being innocent and not "phony." Another similarity between both figures is their non- conventional path through schooling. Both were thrown out of many different learning institutions. This reflects how both understand "truth" as existing outside of formal structures. Salinger's emphasis on Buddhism reflects this and Holden finds nothing but insincerity in the establishment.
I tend to think that their greatest parallel lies in how they view society. Holden is fundamentally unable to conform to what society demands of him and what is asked of him. He cannot accept the "phonies" and hypocrisy that is so intrinsic to the world around him. In Salinger's case, a fierce defense of his privacy indicated that he, too, did not find comfort in the conformist notion of society. Both characters cannot seem to freely interact with the world around them, choosing their own form of retreat. Isolation is Salinger's approach, while disdain is Holden's.
Although Holden is a fictional character and thus different from Salinger in many ways, such as being too young to have served in World War II (as the author did), they share striking similarities. Both come from New York City and a financially well-to-do background. Both attend expensive boarding schools, but are disinterested in doing well academically. Like Holden, Salinger cycled through several schools. However, both are highly intelligent, and have a deep interest in literature and writing. English is the one class Holden has passed in boarding school as his New York odyssey begins. His roommate wants Holden to write a paper for him, because he knows Holden is a good writer. Salinger, of course, became a writer.
Both have what F. Scott Fitzgerald might have called a "heightened sensitivity" to the world around them. They perceive themselves as unable to fit in with the rest of society. As a result, Holden has a breakdown and Salinger ended up a recluse.