In Indiana Jones and the Peril at Delphi we learn that Indy was the first archaeologist to discover and work on translating the Omphalos, a fabled stone that represents the 'navel of the world' in Greek mythology. His mentor advises him that he can spend a year studying it as an object and translating its text and a further year contextualising the tablet and writing his thesis.
Belecamus pushed her plate to the side. "Look, Indy, if the tablet that has been discovered at Delphi is important, and I have the feeling it is, you'll be able to use it as the basis for your Ph.D. With your background, I'd say you can have your doctorate easily in two years. One year of intense study, then your thesis, and you'll be an archaeologist. If it doesn't work out, you fall back on linguistics."
While we have no specific (canon) description of his PhD work, I suspect that the study title would be something along the lines of
"An ethnographic and translative study of the Delphic Omphalos"
Since that basically describes (in fancy terms) what he's just been told to do.