Three instances, really. Hmm... no, four. I loved how uneasy they were around each other. Mara's all genuinely confused at this animosity, since she has no desire to be higher in the Emperor's favor, but there's basically no chance that she could reconcile with him. She has almost an outsider's perspective on Vader and the Emperor and sees them both as a little obsessed with Rebels; at the time she really and truly believes that the Empire is good and right but there's this little critical edge. That part where she tells Vader that he has the entire Five-Oh-First and he should let her keep her Hand of Judgment made me so happy. And at the end, where he actually asks for her assessment of Disra and she wants him to watch Ozzel carefully! I like that they've got that kind of working relationship that's all hostile and nasty one moment and professional, almost friendly, later.
I would so read a story where they had to work together. Anyone read fanfic? I saw one once where Vader met a very young Mara and sort of accidentally got the Emperor to take her as a Hand, but I was meh on it. Vader fics should characterize him like The Sith Who Brought Life Day, which is as close to canon personality as any fic I've seen. (This starts as a humor fic, becomes dramatic, and is awesome.)