Which e-mail address should I give for a recommender in an application?
I know some universities that prefer email addresses that demonstrate the university affiliations of your referees, so that they know the letters will actually come from the listed referees rather than the student pretending to be the referees with a free gmail account. If the referee has multiple university affiliations, then I would recommend the one associated with the university in which you and the referee became acquainted with each other. For example, if you did an internship with a professor at university B, even though the professor holds a tenure position at university A as well, it is better to use the email address of university B in such a situation.

Of course, some professors do not use the mail account provided by the universities, and thus you should consult with your referee first to make sure that you give the email address that the referee actually checks.