In the Majora's Mask story, when Tatl actually sounds worried about Link after he gets thrown far from an attack, despite already being aware of his stupidity.
Though she may have just done it to hurt Link, Gohma giving him a hug near the end of Majora's Mask.
Another one from Gohma was during the second-to-last chapter, when Ganondorf is quite obviously about to kill Link. Gohma, instead of just leaving it alone since Link is no longer useful to her, knocks Ganondorf out and saves Link's life.
The interactions between Diababa and Stallord are subtle moments of this kind.