Bob's nickname was “Elvis,” a 'reference to' the way he styled his hair. [=people called Bob “Elvis” because he styled his hair in the same way Elvis Presley did]
The course covers ancient history 'with' special 'reference to' the Roman Empire. [=the course is about ancient history and especially about the Roman Empire]
I have something further to add 'with reference to' [='with respect to', 'in regard to'] what was said earlier.
(..) l asked. Is there any chance, any chance at all... that I might not be the guy in the prophecy? The Oracle references a half-blood of the eldest gods. You are the only living half-blood heir of Zeus, Hades or Poseidon. The prophecy could refer only to you. What if I destroy Olympus... (..)2013 Percy Jackson: Sea of Monsters