Hard to pick one. I always liked the odd ones. My fave has to go with "Eleanor Rigby", though. I consider it to be one of the earliest hits of prog, disguised as pop.
Others are "Can't Buy Me Love" (which they put on the Hey Jude release, and was great counterpoint to the new material), "And Your Bird Can Sing", "While My Guitar Gently Weeps", "Taxman", "Drive My Car", "Hey, Bulldog" and others...
And perhaps the greatest Beatles bass line ever...