For Simon and Garfunkel, it really comes down to Bridge over Troubled Water, Mrs. Robinson and The Boxer for me, and I'm going with The Boxer in somewhat of an easy decision.
As for the Beatles, Yesterday is probably the general pick, but I'm going with Hey Jude. It's such a dramatic piece of music with such emotion and "flare" in it.
Bob Dylan? Tough one. So many greats, Like A Rolling Stone is timeless, but I'd probably go with Subterranean Homesick Blues, that song, IMO, really defines that era of music.
Beach Boys? I'm going with God Only Knows.