Guest stars John Billingsley and Susanna Thompson both had significant roles in the Star Trek universe. Billingsley was Dr Phlox in Star Trek: Enterprise (2001), and Thompson was the Borg Queen on Star Trek: Voyager (1995).
The second clue that Tony is undercover while dating Jeanne happens. When Jeanne finds an apartment for them to move into, she mentions it's not far from the hospital (where she works) and the University. Tony's cover job is a university professor.