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.
(..) wind up implanting eggs in my chest or something... and I eat one of you, I'm sorry. I do not want another single pop culture reference out of you for the rest of the trip. You understand? I'm trying to say that something is coming. Thanos! (..)2018 Avengers: Infinity War